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