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.ws.sifts.SiftsSettings;
  34
  35 import java.awt.BorderLayout;
  36 import java.awt.Color;
  37 import java.awt.Dimension;
  38 import java.awt.Font;
  39 import java.awt.event.ActionEvent;
  40 import java.awt.event.ActionListener;
  41 import java.awt.event.MouseEvent;
  42 import java.io.File;
  43 import java.util.Collection;
  44 import java.util.List;
  45 import java.util.StringTokenizer;
  46 import java.util.Vector;
  47
  48 import javax.help.HelpSetException;
  49 import javax.swing.JColorChooser;
  50 import javax.swing.JFileChooser;
  51 import javax.swing.JInternalFrame;
  52 import javax.swing.JOptionPane;
  53 import javax.swing.JPanel;
  54
  55 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  56
  57 /**
  58  * DOCUMENT ME!
  59  *
  60  * @author $author$
  61  * @version $Revision$
  62  */
  63 public class Preferences extends GPreferences
  64 {
  65   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
  66
  67   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
  68
  69   public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
  70
  71   public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
  72
  73   public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
  74
  75   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  76
  77   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  78
  79   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  80
  81   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  82
  83   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  84
  85   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  86
  87   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  88
  89   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  90
  91   private static final int MIN_FONT_SIZE = 1;
  92
  93   private static final int MAX_FONT_SIZE = 30;
  94
  95   /**
  96    * Holds name and link separated with | character. Sequence ID must be
  97    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
  98    */
  99   public static Vector sequenceURLLinks;
 100
 101   /**
 102    * Holds name and link separated with | character. Sequence IDS and Sequences
 103    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
 104    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
 105    * for first and second token specified after a pipe character at end |,|.
 106    * (TODO: proper escape for using | to separate ids or sequences
 107    */
 108
 109   public static Vector groupURLLinks;
 110   static
 111   {
 112     String string = Cache
 113             .getDefault(
 114                     "SEQUENCE_LINKS",
 115                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
 116     sequenceURLLinks = new Vector();
 117
 118     try
 119     {
 120       StringTokenizer st = new StringTokenizer(string, "|");
 121       while (st.hasMoreElements())
 122       {
 123         String name = st.nextToken();
 124         String url = st.nextToken();
 125         // check for '|' within a regex
 126         int rxstart = url.indexOf("$SEQUENCE_ID$");
 127         while (rxstart == -1 && url.indexOf("/=$") == -1)
 128         {
 129           url = url + "|" + st.nextToken();
 130         }
 131         sequenceURLLinks.addElement(name + "|" + url);
 132       }
 133     } catch (Exception ex)
 134     {
 135       System.out.println(ex + "\nError parsing sequence links");
 136     }
 137     {
 138       // upgrade old SRS link
 139       int srsPos = sequenceURLLinks
 140               .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
 141       if (srsPos > -1)
 142       {
 143         sequenceURLLinks
 144                 .setElementAt(
 145                         "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
 146                         srsPos);
 147       }
 148     }
 149
 150     /**
 151      * TODO: reformulate groupURL encoding so two or more can be stored in the
 152      * .properties file as '|' separated strings
 153      */
 154
 155     groupURLLinks = new Vector();
 156   }
 157
 158   Vector nameLinks, urlLinks;
 159
 160   JInternalFrame frame;
 161
 162   DasSourceBrowser dasSource;
 163
 164   private WsPreferences wsPrefs;
 165
 166   /**
 167    * Creates a new Preferences object.
 168    */
 169   public Preferences()
 170   {
 171     super();
 172     frame = new JInternalFrame();
 173     frame.setContentPane(this);
 174     dasSource = new DasSourceBrowser();
 175     dasTab.add(dasSource, BorderLayout.CENTER);
 176     wsPrefs = new WsPreferences();
 177     wsTab.add(wsPrefs, BorderLayout.CENTER);
 178     int width = 500, height = 450;
 179     if (new jalview.util.Platform().isAMac())
 180     {
 181       width = 570;
 182       height = 480;
 183     }
 184
 185     Desktop.addInternalFrame(frame,
 186             MessageManager.getString("label.preferences"), width, height);
 187     frame.setMinimumSize(new Dimension(width, height));
 188
 189     /*
 190      * Set Visual tab defaults
 191      */
 192     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 193     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 194     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 195     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 196
 197     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 198     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 199     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 200     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 201     showUnconserved
 202             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 203     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 204             false));
 205     showGroupConservation.setSelected(Cache.getDefault(
 206             "SHOW_GROUP_CONSERVATION", false));
 207     showConsensHistogram.setSelected(Cache.getDefault(
 208             "SHOW_CONSENSUS_HISTOGRAM", true));
 209     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 210             false));
 211     showNpTooltip.setSelected(Cache
 212             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 213     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 214             true));
 215
 216     String[] fonts = java.awt.GraphicsEnvironment
 217             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 218     for (int i = 0; i < fonts.length; i++)
 219     {
 220       fontNameCB.addItem(fonts[i]);
 221     }
 222
 223     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 224     {
 225       fontSizeCB.addItem(i + "");
 226     }
 227
 228     fontStyleCB.addItem("plain");
 229     fontStyleCB.addItem("bold");
 230     fontStyleCB.addItem("italic");
 231
 232     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 233     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 234     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 235             + ""));
 236
 237     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 238     scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
 239             false));
 240
 241     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 242
 243     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 244
 245     gapSymbolCB.addItem("-");
 246     gapSymbolCB.addItem(".");
 247
 248     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 249
 250     sortby.addItem("No sort");
 251     sortby.addItem("Id");
 252     sortby.addItem("Pairwise Identity");
 253     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 254
 255     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 256     sortAnnBy
 257             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 258     sortAnnBy
 259             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 260     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 261             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 262                     SequenceAnnotationOrder.NONE.name()));
 263     sortAnnBy.setSelectedItem(savedSort.toString());
 264
 265     sortAutocalc.addItem("Autocalculated first");
 266     sortAutocalc.addItem("Autocalculated last");
 267     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
 268     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 269             : sortAutocalc.getItemAt(1));
 270     startupCheckbox
 271             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 272     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 273             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 274                     + "/examples/exampleFile_2_3.jar"));
 275
 276     /*
 277      * Set Colours tab defaults
 278      */
 279     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 280     {
 281       protColour.addItem(ColourSchemeProperty.getColourName(i));
 282       nucColour.addItem(ColourSchemeProperty.getColourName(i));
 283     }
 284     String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
 285     String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
 286     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
 287     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
 288     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
 289     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 290             Color.orange));
 291     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 292             Color.red));
 293
 294     /*
 295      * Set Structure tab defaults.
 296      */
 297     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 298     structFromPdb.setSelected(structSelected);
 299     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 300     useRnaView.setEnabled(structSelected);
 301     addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
 302     addSecondaryStructure.setEnabled(structSelected);
 303     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 304     addTempFactor.setEnabled(structSelected);
 305     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 306             ViewerType.JMOL.name()));
 307     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 308     chimeraPath.addActionListener(new ActionListener()
 309     {
 310       @Override
 311       public void actionPerformed(ActionEvent e)
 312       {
 313         validateChimeraPath();
 314       }
 315     });
 316
 317     if (Cache.getDefault("MAP_WITH_SIFTS", false))
 318     {
 319       siftsMapping.setSelected(true);
 320     }
 321     else
 322     {
 323       nwMapping.setSelected(true);
 324     }
 325
 326     SiftsSettings
 327             .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
 328
 329     /*
 330      * Set Connections tab defaults
 331      */
 332     nameLinks = new Vector();
 333     urlLinks = new Vector();
 334     for (int i = 0; i < sequenceURLLinks.size(); i++)
 335     {
 336       String link = sequenceURLLinks.elementAt(i).toString();
 337       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 338       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 339     }
 340
 341     updateLinkData();
 342
 343     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 344     proxyServerTB.setEnabled(useProxy.isSelected());
 345     proxyPortTB.setEnabled(useProxy.isSelected());
 346     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 347     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 348
 349     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 350
 351     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 352     // note antisense here: default is true
 353     questionnaire
 354             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 355     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 356
 357     /*
 358      * Set Output tab defaults
 359      */
 360     epsRendering
 361             .addItem(MessageManager.getString("label.prompt_each_time"));
 362     epsRendering.addItem(MessageManager.getString("label.lineart"));
 363     epsRendering.addItem(MessageManager.getString("action.text"));
 364     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 365             "Prompt each time"));
 366     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 367     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 368     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 369     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 370     userIdWidth.setText(wi == null ? "" : wi.toString());
 371     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 372     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 373     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 374     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 375     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 376     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 377     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 378     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 379     embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
 380             true));
 381
 382     /*
 383      * Set Editing tab defaults
 384      */
 385     autoCalculateConsCheck.setSelected(Cache.getDefault(
 386             "AUTO_CALC_CONSENSUS", true));
 387     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 388     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 389
 390     annotations_actionPerformed(null); // update the display of the annotation
 391                                        // settings
 392   }
 393
 394   /**
 395    * Save user selections on the Preferences tabs to the Cache and write out to
 396    * file.
 397    *
 398    * @param e
 399    */
 400   @Override
 401   public void ok_actionPerformed(ActionEvent e)
 402   {
 403     if (!validateSettings())
 404     {
 405       return;
 406     }
 407
 408     /*
 409      * Save Visual settings
 410      */
 411     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 412             Boolean.toString(seqLimit.isSelected()));
 413     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 414             Boolean.toString(rightAlign.isSelected()));
 415     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 416             Boolean.toString(fullScreen.isSelected()));
 417     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 418             Boolean.toString(openoverv.isSelected()));
 419     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 420             Boolean.toString(annotations.isSelected()));
 421     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 422             Boolean.toString(conservation.isSelected()));
 423     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 424             Boolean.toString(quality.isSelected()));
 425     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 426             Boolean.toString(identity.isSelected()));
 427
 428     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 429             .getSelectedItem().toString());
 430
 431     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 432             .getSelectedItem().toString());
 433     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 434             .getSelectedItem().toString());
 435     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 436             .getSelectedItem().toString());
 437
 438     Cache.applicationProperties.setProperty("ID_ITALICS",
 439             Boolean.toString(idItalics.isSelected()));
 440     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 441             Boolean.toString(showUnconserved.isSelected()));
 442     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 443             Boolean.toString(showGroupConsensus.isSelected()));
 444     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 445             Boolean.toString(showGroupConservation.isSelected()));
 446     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 447             Boolean.toString(showConsensHistogram.isSelected()));
 448     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 449             Boolean.toString(showConsensLogo.isSelected()));
 450     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 451             Boolean.toString(smoothFont.isSelected()));
 452     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
 453             Boolean.toString(scaleProteinToCdna.isSelected()));
 454     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 455             Boolean.toString(showNpTooltip.isSelected()));
 456     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 457             Boolean.toString(showDbRefTooltip.isSelected()));
 458
 459     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 460             Boolean.toString(wrap.isSelected()));
 461
 462     Cache.applicationProperties.setProperty("STARTUP_FILE",
 463             startupFileTextfield.getText());
 464     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 465             Boolean.toString(startupCheckbox.isSelected()));
 466
 467     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 468             .getSelectedItem().toString());
 469
 470     // convert description of sort order to enum name for save
 471     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 472             .forDescription(sortAnnBy.getSelectedItem().toString());
 473     if (annSortOrder != null)
 474     {
 475       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 476               annSortOrder.name());
 477     }
 478
 479     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 480     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
 481             .valueOf(showAutocalcFirst).toString());
 482
 483     /*
 484      * Save Colours settings
 485      */
 486     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
 487             .getSelectedItem().toString());
 488     Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
 489             .getSelectedItem().toString());
 490     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 491             minColour.getBackground());
 492     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 493             maxColour.getBackground());
 494
 495     /*
 496      * Save Structure settings
 497      */
 498     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 499             Boolean.toString(addTempFactor.isSelected()));
 500     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 501             Boolean.toString(addSecondaryStructure.isSelected()));
 502     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 503             Boolean.toString(useRnaView.isSelected()));
 504     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 505             Boolean.toString(structFromPdb.isSelected()));
 506     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 507             .getSelectedItem().toString());
 508     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 509     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
 510             Boolean.toString(siftsMapping.isSelected()));
 511     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
 512
 513     /*
 514      * Save Output settings
 515      */
 516     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 517     {
 518       Cache.applicationProperties.remove("EPS_RENDERING");
 519     }
 520     else
 521     {
 522       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 523               .getSelectedItem().toString());
 524     }
 525
 526     /*
 527      * Save Connections settings
 528      */
 529     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 530
 531     jalview.util.BrowserLauncher.resetBrowser();
 532
 533     if (nameLinks.size() > 0)
 534     {
 535       StringBuffer links = new StringBuffer();
 536       sequenceURLLinks = new Vector();
 537       for (int i = 0; i < nameLinks.size(); i++)
 538       {
 539         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 540                 + urlLinks.elementAt(i));
 541         links.append(sequenceURLLinks.elementAt(i).toString());
 542         links.append("|");
 543       }
 544       // remove last "|"
 545       links.setLength(links.length() - 1);
 546       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 547               links.toString());
 548     }
 549     else
 550     {
 551       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 552     }
 553
 554     Cache.applicationProperties.setProperty("USE_PROXY",
 555             Boolean.toString(useProxy.isSelected()));
 556
 557     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 558
 559     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 560
 561     if (useProxy.isSelected())
 562     {
 563       System.setProperty("http.proxyHost", proxyServerTB.getText());
 564       System.setProperty("http.proxyPort", proxyPortTB.getText());
 565     }
 566     else
 567     {
 568       System.setProperty("http.proxyHost", "");
 569       System.setProperty("http.proxyPort", "");
 570     }
 571     Cache.setProperty("VERSION_CHECK",
 572             Boolean.toString(versioncheck.isSelected()));
 573     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 574     {
 575       // default is false - we only set this if the user has actively agreed
 576       Cache.setProperty("USAGESTATS",
 577               Boolean.toString(usagestats.isSelected()));
 578     }
 579     if (!questionnaire.isSelected())
 580     {
 581       Cache.setProperty("NOQUESTIONNAIRES", "true");
 582     }
 583     else
 584     {
 585       // special - made easy to edit a property file to disable questionnaires
 586       // by just adding the given line
 587       Cache.removeProperty("NOQUESTIONNAIRES");
 588     }
 589
 590     /*
 591      * Save Output settings
 592      */
 593     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 594             Boolean.toString(blcjv.isSelected()));
 595     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 596             Boolean.toString(clustaljv.isSelected()));
 597     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 598             Boolean.toString(fastajv.isSelected()));
 599     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 600             Boolean.toString(msfjv.isSelected()));
 601     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 602             Boolean.toString(pfamjv.isSelected()));
 603     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 604             Boolean.toString(pileupjv.isSelected()));
 605     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 606             Boolean.toString(pirjv.isSelected()));
 607     Cache.applicationProperties.setProperty("PIR_MODELLER",
 608             Boolean.toString(modellerOutput.isSelected()));
 609     Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
 610             Boolean.toString(embbedBioJSON.isSelected()));
 611     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 612
 613     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 614             Boolean.toString(autoIdWidth.isSelected()));
 615     userIdWidth_actionPerformed();
 616     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 617             userIdWidth.getText());
 618
 619     /*
 620      * Save Editing settings
 621      */
 622     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 623             Boolean.toString(autoCalculateConsCheck.isSelected()));
 624     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 625             Boolean.toString(sortByTree.isSelected()));
 626     Cache.applicationProperties.setProperty("PAD_GAPS",
 627             Boolean.toString(padGaps.isSelected()));
 628
 629     dasSource.saveProperties(Cache.applicationProperties);
 630     wsPrefs.updateAndRefreshWsMenuConfig(false);
 631     Cache.saveProperties();
 632     Desktop.instance.doConfigureStructurePrefs();
 633     try
 634     {
 635       frame.setClosed(true);
 636     } catch (Exception ex)
 637     {
 638     }
 639   }
 640
 641   /**
 642    * Do any necessary validation before saving settings. Return focus to the
 643    * first tab which fails validation.
 644    *
 645    * @return
 646    */
 647   private boolean validateSettings()
 648   {
 649     if (!validateStructure())
 650     {
 651       structureTab.requestFocusInWindow();
 652       return false;
 653     }
 654     return true;
 655   }
 656
 657   @Override
 658   protected boolean validateStructure()
 659   {
 660     return validateChimeraPath();
 661
 662   }
 663
 664   /**
 665    * DOCUMENT ME!
 666    */
 667   @Override
 668   public void startupFileTextfield_mouseClicked()
 669   {
 670     JalviewFileChooser chooser = new JalviewFileChooser(
 671             jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
 672                 "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
 673                 "jar" }, new String[] { "Fasta", "Clustal", "PFAM", "MSF",
 674                 "PIR", "BLC", "Jalview" },
 675             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 676     chooser.setFileView(new JalviewFileView());
 677     chooser.setDialogTitle(MessageManager
 678             .getString("label.select_startup_file"));
 679
 680     int value = chooser.showOpenDialog(this);
 681
 682     if (value == JalviewFileChooser.APPROVE_OPTION)
 683     {
 684       jalview.bin.Cache.applicationProperties.setProperty(
 685               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 686       startupFileTextfield.setText(chooser.getSelectedFile()
 687               .getAbsolutePath());
 688     }
 689   }
 690
 691   /**
 692    * DOCUMENT ME!
 693    *
 694    * @param e
 695    *          DOCUMENT ME!
 696    */
 697   @Override
 698   public void cancel_actionPerformed(ActionEvent e)
 699   {
 700     try
 701     {
 702       wsPrefs.updateWsMenuConfig(true);
 703       wsPrefs.refreshWs_actionPerformed(e);
 704       frame.setClosed(true);
 705     } catch (Exception ex)
 706     {
 707     }
 708   }
 709
 710   /**
 711    * DOCUMENT ME!
 712    *
 713    * @param e
 714    *          DOCUMENT ME!
 715    */
 716   @Override
 717   public void annotations_actionPerformed(ActionEvent e)
 718   {
 719     conservation.setEnabled(annotations.isSelected());
 720     quality.setEnabled(annotations.isSelected());
 721     identity.setEnabled(annotations.isSelected());
 722     showGroupConsensus.setEnabled(annotations.isSelected());
 723     showGroupConservation.setEnabled(annotations.isSelected());
 724     showConsensHistogram.setEnabled(annotations.isSelected()
 725             && (identity.isSelected() || showGroupConsensus.isSelected()));
 726     showConsensLogo.setEnabled(annotations.isSelected()
 727             && (identity.isSelected() || showGroupConsensus.isSelected()));
 728   }
 729
 730   @Override
 731   public void newLink_actionPerformed(ActionEvent e)
 732   {
 733
 734     GSequenceLink link = new GSequenceLink();
 735     boolean valid = false;
 736     while (!valid)
 737     {
 738       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 739               MessageManager.getString("label.new_sequence_url_link"),
 740               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 741       {
 742         if (link.checkValid())
 743         {
 744           nameLinks.addElement(link.getName());
 745           urlLinks.addElement(link.getURL());
 746           updateLinkData();
 747           valid = true;
 748         }
 749       }
 750       else
 751       {
 752         break;
 753       }
 754     }
 755   }
 756
 757   @Override
 758   public void editLink_actionPerformed(ActionEvent e)
 759   {
 760     GSequenceLink link = new GSequenceLink();
 761
 762     int index = linkNameList.getSelectedIndex();
 763     if (index == -1)
 764     {
 765       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 766               MessageManager.getString("label.no_link_selected"),
 767               MessageManager.getString("label.no_link_selected"),
 768               JOptionPane.WARNING_MESSAGE);
 769       return;
 770     }
 771
 772     link.setName(nameLinks.elementAt(index).toString());
 773     link.setURL(urlLinks.elementAt(index).toString());
 774
 775     boolean valid = false;
 776     while (!valid)
 777     {
 778
 779       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 780               MessageManager.getString("label.new_sequence_url_link"),
 781               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 782       {
 783         if (link.checkValid())
 784         {
 785           nameLinks.setElementAt(link.getName(), index);
 786           urlLinks.setElementAt(link.getURL(), index);
 787           updateLinkData();
 788           valid = true;
 789         }
 790       }
 791
 792       else
 793       {
 794         break;
 795       }
 796     }
 797   }
 798
 799   @Override
 800   public void deleteLink_actionPerformed(ActionEvent e)
 801   {
 802     int index = linkNameList.getSelectedIndex();
 803     if (index == -1)
 804     {
 805       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 806               MessageManager.getString("label.no_link_selected"),
 807               MessageManager.getString("label.no_link_selected"),
 808               JOptionPane.WARNING_MESSAGE);
 809       return;
 810     }
 811     nameLinks.removeElementAt(index);
 812     urlLinks.removeElementAt(index);
 813     updateLinkData();
 814   }
 815
 816   void updateLinkData()
 817   {
 818     linkNameList.setListData(nameLinks);
 819     linkURLList.setListData(urlLinks);
 820   }
 821
 822   @Override
 823   public void defaultBrowser_mouseClicked(MouseEvent e)
 824   {
 825     JFileChooser chooser = new JFileChooser(".");
 826     chooser.setDialogTitle(MessageManager
 827             .getString("label.select_default_browser"));
 828
 829     int value = chooser.showOpenDialog(this);
 830
 831     if (value == JFileChooser.APPROVE_OPTION)
 832     {
 833       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 834     }
 835
 836   }
 837
 838   /*
 839    * (non-Javadoc)
 840    *
 841    * @see
 842    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 843    * .ActionEvent)
 844    */
 845   @Override
 846   protected void showunconserved_actionPerformed(ActionEvent e)
 847   {
 848     // TODO Auto-generated method stub
 849     super.showunconserved_actionPerformed(e);
 850   }
 851
 852   public static Collection getGroupURLLinks()
 853   {
 854     return groupURLLinks;
 855   }
 856
 857   @Override
 858   public void minColour_actionPerformed(JPanel panel)
 859   {
 860     Color col = JColorChooser.showDialog(this,
 861             MessageManager.getString("label.select_colour_minimum_value"),
 862             minColour.getBackground());
 863     if (col != null)
 864     {
 865       panel.setBackground(col);
 866     }
 867     panel.repaint();
 868   }
 869
 870   @Override
 871   public void maxColour_actionPerformed(JPanel panel)
 872   {
 873     Color col = JColorChooser.showDialog(this,
 874             MessageManager.getString("label.select_colour_maximum_value"),
 875             maxColour.getBackground());
 876     if (col != null)
 877     {
 878       panel.setBackground(col);
 879     }
 880     panel.repaint();
 881   }
 882
 883   @Override
 884   protected void userIdWidth_actionPerformed()
 885   {
 886     try
 887     {
 888       String val = userIdWidth.getText().trim();
 889       if (val.length() > 0)
 890       {
 891         Integer iw = Integer.parseInt(val);
 892         if (iw.intValue() < 12)
 893         {
 894           throw new NumberFormatException();
 895         }
 896         userIdWidth.setText(iw.toString());
 897       }
 898     } catch (NumberFormatException x)
 899     {
 900       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
 901               .getString("warn.user_defined_width_requirements"),
 902               MessageManager.getString("label.invalid_id_column_width"),
 903               JOptionPane.WARNING_MESSAGE);
 904       userIdWidth.setText("");
 905     }
 906   }
 907
 908   @Override
 909   protected void autoIdWidth_actionPerformed()
 910   {
 911     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 912     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 913   }
 914
 915   /**
 916    * Returns true if chimera path is to a valid executable, else show an error
 917    * dialog.
 918    */
 919   private boolean validateChimeraPath()
 920   {
 921     if (chimeraPath.getText().trim().length() > 0)
 922     {
 923       File f = new File(chimeraPath.getText());
 924       if (!f.canExecute())
 925       {
 926         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 927                 MessageManager.getString("label.invalid_chimera_path"),
 928                 MessageManager.getString("label.invalid_name"),
 929                 JOptionPane.ERROR_MESSAGE);
 930         return false;
 931       }
 932     }
 933     return true;
 934   }
 935
 936   /**
 937    * If Chimera is selected, check it can be found on default or user-specified
 938    * path, if not show a warning/help dialog.
 939    */
 940   @Override
 941   protected void structureViewer_actionPerformed(String selectedItem)
 942   {
 943     if (!selectedItem.equals(ViewerType.CHIMERA.name()))
 944     {
 945       return;
 946     }
 947     boolean found = false;
 948
 949     /*
 950      * Try user-specified and standard paths for Chimera executable.
 951      */
 952     List<String> paths = StructureManager.getChimeraPaths();
 953     paths.add(0, chimeraPath.getText());
 954     for (String path : paths)
 955     {
 956       if (new File(path.trim()).canExecute())
 957       {
 958         found = true;
 959         break;
 960       }
 961     }
 962     if (!found)
 963     {
 964       String[] options = { "OK", "Help" };
 965       int showHelp = JOptionPane.showInternalOptionDialog(
 966               Desktop.desktop,
 967               JvSwingUtils.wrapTooltip(true,
 968                       MessageManager.getString("label.chimera_missing")),
 969               "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
 970               null, options, options[0]);
 971       if (showHelp == JOptionPane.NO_OPTION)
 972       {
 973         try
 974         {
 975           Help.showHelpWindow(HelpId.StructureViewer);
 976         } catch (HelpSetException e)
 977         {
 978           e.printStackTrace();
 979         }
 980       }
 981     }
 982   }
 983
 984 }