src/jalview/gui/Preferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   3  * Copyright (C) 2014 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.Viewer;
  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 ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
  66
  67   public static final String ADD_SS_ANN = "ADD_SS_ANN";
  68
  69   public static final String USE_RNAVIEW = "USE_RNAVIEW";
  70
  71   public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
  72
  73   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
  74
  75   public static final String CHIMERA_PATH = "CHIMERA_PATH";
  76
  77   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
  78
  79   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
  80
  81   private static final int MIN_FONT_SIZE = 1;
  82
  83   private static final int MAX_FONT_SIZE = 30;
  84
  85   /**
  86    * Holds name and link separated with | character. Sequence ID must be
  87    * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
  88    */
  89   public static Vector sequenceURLLinks;
  90
  91   /**
  92    * Holds name and link separated with | character. Sequence IDS and Sequences
  93    * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
  94    * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
  95    * for first and second token specified after a pipe character at end |,|.
  96    * (TODO: proper escape for using | to separate ids or sequences
  97    */
  98
  99   public static Vector groupURLLinks;
 100   static
 101   {
 102     String string = Cache
 103             .getDefault(
 104                     "SEQUENCE_LINKS",
 105                     "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
 106     sequenceURLLinks = new Vector();
 107
 108     try
 109     {
 110       StringTokenizer st = new StringTokenizer(string, "|");
 111       while (st.hasMoreElements())
 112       {
 113         String name = st.nextToken();
 114         String url = st.nextToken();
 115         // check for '|' within a regex
 116         int rxstart = url.indexOf("$SEQUENCE_ID$");
 117         while (rxstart == -1 && url.indexOf("/=$") == -1)
 118         {
 119           url = url + "|" + st.nextToken();
 120         }
 121         sequenceURLLinks.addElement(name + "|" + url);
 122       }
 123     } catch (Exception ex)
 124     {
 125       System.out.println(ex + "\nError parsing sequence links");
 126     }
 127     {
 128       // upgrade old SRS link
 129       int srsPos = sequenceURLLinks
 130               .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
 131       if (srsPos > -1)
 132       {
 133         sequenceURLLinks
 134                 .setElementAt(
 135                         "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
 136                         srsPos);
 137       }
 138     }
 139
 140     /**
 141      * TODO: reformulate groupURL encoding so two or more can be stored in the
 142      * .properties file as '|' separated strings
 143      */
 144
 145     groupURLLinks = new Vector();
 146   }
 147
 148   Vector nameLinks, urlLinks;
 149
 150   JInternalFrame frame;
 151
 152   DasSourceBrowser dasSource;
 153
 154   private WsPreferences wsPrefs;
 155
 156   /**
 157    * Creates a new Preferences object.
 158    */
 159   public Preferences()
 160   {
 161     super();
 162     frame = new JInternalFrame();
 163     frame.setContentPane(this);
 164     dasSource = new DasSourceBrowser();
 165     dasTab.add(dasSource, BorderLayout.CENTER);
 166     wsPrefs = new WsPreferences();
 167     wsTab.add(wsPrefs, BorderLayout.CENTER);
 168     int width = 500, height = 420;
 169     if (new jalview.util.Platform().isAMac())
 170     {
 171       width = 570;
 172       height = 460;
 173     }
 174
 175     Desktop.addInternalFrame(frame,
 176             MessageManager.getString("label.preferences"), width, height);
 177     frame.setMinimumSize(new Dimension(width, height));
 178
 179     /*
 180      * Set Visual tab defaults
 181      */
 182     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
 183     rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
 184     fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
 185     annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
 186
 187     conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
 188     quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
 189     identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
 190     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
 191     showUnconserved
 192             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
 193     showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
 194             false));
 195     showGroupConservation.setSelected(Cache.getDefault(
 196             "SHOW_GROUP_CONSERVATION", false));
 197     showConsensHistogram.setSelected(Cache.getDefault(
 198             "SHOW_CONSENSUS_HISTOGRAM", true));
 199     showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
 200             false));
 201     showNpTooltip.setSelected(Cache
 202             .getDefault("SHOW_NPFEATS_TOOLTIP", true));
 203     showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
 204             true));
 205
 206     String[] fonts = java.awt.GraphicsEnvironment
 207             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 208     for (int i = 0; i < fonts.length; i++)
 209     {
 210       fontNameCB.addItem(fonts[i]);
 211     }
 212
 213     for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
 214     {
 215       fontSizeCB.addItem(i + "");
 216     }
 217
 218     fontStyleCB.addItem("plain");
 219     fontStyleCB.addItem("bold");
 220     fontStyleCB.addItem("italic");
 221
 222     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
 223     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
 224     fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
 225             + ""));
 226
 227     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 228
 229     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 230
 231     wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 232
 233     gapSymbolCB.addItem("-");
 234     gapSymbolCB.addItem(".");
 235
 236     gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 237
 238     sortby.addItem("No sort");
 239     sortby.addItem("Id");
 240     sortby.addItem("Pairwise Identity");
 241     sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 242
 243     sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
 244     sortAnnBy
 245             .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
 246     sortAnnBy
 247             .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
 248     SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
 249             .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
 250                     SequenceAnnotationOrder.NONE.name()));
 251     sortAnnBy.setSelectedItem(savedSort.toString());
 252
 253     sortAutocalc.addItem("Autocalculated first");
 254     sortAutocalc.addItem("Autocalculated last");
 255     final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE,
 256             true);
 257     sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
 258             : sortAutocalc.getItemAt(1));
 259     startupCheckbox
 260             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
 261     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
 262             Cache.getDefault("www.jalview.org", "http://www.jalview.org")
 263                     + "/examples/exampleFile_2_3.jar"));
 264
 265     /*
 266      * Set Colours tab defaults
 267      */
 268     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
 269     {
 270       colour.addItem(ColourSchemeProperty.getColourName(i));
 271     }
 272     String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 273     colour.setSelectedItem(string);
 274     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 275             Color.orange));
 276     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 277             Color.red));
 278
 279     /*
 280      * Set Structure tab defaults.
 281      */
 282     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
 283     structFromPdb.setSelected(structSelected);
 284     useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
 285     useRnaView.setEnabled(structSelected);
 286     addSecondaryStructure
 287             .setSelected(Cache.getDefault(ADD_SS_ANN, false));
 288     addSecondaryStructure.setEnabled(structSelected);
 289     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
 290     addTempFactor.setEnabled(structSelected);
 291     structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
 292             Viewer.JMOL.name()));
 293     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
 294     chimeraPath.addActionListener(new ActionListener()
 295     {
 296       @Override
 297       public void actionPerformed(ActionEvent e)
 298       {
 299         validateChimeraPath();
 300       }
 301     });
 302
 303     /*
 304      * Set Connections tab defaults
 305      */
 306     nameLinks = new Vector();
 307     urlLinks = new Vector();
 308     for (int i = 0; i < sequenceURLLinks.size(); i++)
 309     {
 310       String link = sequenceURLLinks.elementAt(i).toString();
 311       nameLinks.addElement(link.substring(0, link.indexOf("|")));
 312       urlLinks.addElement(link.substring(link.indexOf("|") + 1));
 313     }
 314
 315     updateLinkData();
 316
 317     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
 318     proxyServerTB.setEnabled(useProxy.isSelected());
 319     proxyPortTB.setEnabled(useProxy.isSelected());
 320     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
 321     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 322
 323     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 324
 325     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
 326     // note antisense here: default is true
 327     questionnaire
 328             .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
 329     versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 330
 331     /*
 332      * Set Output tab defaults
 333      */
 334     epsRendering
 335             .addItem(MessageManager.getString("label.prompt_each_time"));
 336     epsRendering.addItem(MessageManager.getString("label.lineart"));
 337     epsRendering.addItem(MessageManager.getString("action.text"));
 338     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
 339             "Prompt each time"));
 340     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
 341     userIdWidth.setEnabled(autoIdWidth.isSelected());
 342     userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
 343     Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
 344     userIdWidth.setText(wi == null ? "" : wi.toString());
 345     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
 346     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
 347     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
 348     msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
 349     pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
 350     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
 351     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
 352     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
 353
 354     /*
 355      * Set Editing tab defaults
 356      */
 357     autoCalculateConsCheck.setSelected(Cache.getDefault(
 358             "AUTO_CALC_CONSENSUS", true));
 359     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
 360     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 361
 362     annotations_actionPerformed(null); // update the display of the annotation
 363                                        // settings
 364   }
 365
 366   /**
 367    * Save user selections on the Preferences tabs to the Cache and write out to
 368    * file.
 369    *
 370    * @param e
 371    */
 372   public void ok_actionPerformed(ActionEvent e)
 373   {
 374     if (!validateSettings())
 375     {
 376       return;
 377     }
 378
 379     /*
 380      * Save Visual settings
 381      */
 382     Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
 383             Boolean.toString(seqLimit.isSelected()));
 384     Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
 385             Boolean.toString(rightAlign.isSelected()));
 386     Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
 387             Boolean.toString(fullScreen.isSelected()));
 388     Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
 389             Boolean.toString(openoverv.isSelected()));
 390     Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
 391             Boolean.toString(annotations.isSelected()));
 392     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
 393             Boolean.toString(conservation.isSelected()));
 394     Cache.applicationProperties.setProperty("SHOW_QUALITY",
 395             Boolean.toString(quality.isSelected()));
 396     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
 397             Boolean.toString(identity.isSelected()));
 398
 399     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
 400             .getSelectedItem().toString());
 401
 402     Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
 403             .getSelectedItem().toString());
 404     Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
 405             .getSelectedItem().toString());
 406     Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
 407             .getSelectedItem().toString());
 408
 409     Cache.applicationProperties.setProperty("ID_ITALICS",
 410             Boolean.toString(idItalics.isSelected()));
 411     Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
 412             Boolean.toString(showUnconserved.isSelected()));
 413     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
 414             Boolean.toString(showGroupConsensus.isSelected()));
 415     Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
 416             Boolean.toString(showGroupConservation.isSelected()));
 417     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
 418             Boolean.toString(showConsensHistogram.isSelected()));
 419     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
 420             Boolean.toString(showConsensLogo.isSelected()));
 421     Cache.applicationProperties.setProperty("ANTI_ALIAS",
 422             Boolean.toString(smoothFont.isSelected()));
 423     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
 424             Boolean.toString(showNpTooltip.isSelected()));
 425     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
 426             Boolean.toString(showDbRefTooltip.isSelected()));
 427
 428     Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
 429             Boolean.toString(wrap.isSelected()));
 430
 431     Cache.applicationProperties.setProperty("STARTUP_FILE",
 432             startupFileTextfield.getText());
 433     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
 434             Boolean.toString(startupCheckbox.isSelected()));
 435
 436     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
 437             .getSelectedItem().toString());
 438
 439     // convert description of sort order to enum name for save
 440     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
 441             .forDescription(sortAnnBy.getSelectedItem().toString());
 442     if (annSortOrder != null)
 443     {
 444       Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
 445               annSortOrder.name());
 446     }
 447
 448     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
 449     Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
 450             Boolean.valueOf(showAutocalcFirst).toString());
 451
 452     /*
 453      * Save Colours settings
 454      */
 455     Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
 456             .getSelectedItem().toString());
 457     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
 458             minColour.getBackground());
 459     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
 460             maxColour.getBackground());
 461
 462     /*
 463      * Save Structure settings
 464      */
 465     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
 466             Boolean.toString(addTempFactor.isSelected()));
 467     Cache.applicationProperties.setProperty(ADD_SS_ANN,
 468             Boolean.toString(addSecondaryStructure.isSelected()));
 469     Cache.applicationProperties.setProperty(USE_RNAVIEW,
 470             Boolean.toString(useRnaView.isSelected()));
 471     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
 472             Boolean.toString(structFromPdb.isSelected()));
 473     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
 474             .getSelectedItem().toString());
 475     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
 476
 477     /*
 478      * Save Output settings
 479      */
 480     if (epsRendering.getSelectedItem().equals("Prompt each time"))
 481     {
 482       Cache.applicationProperties.remove("EPS_RENDERING");
 483     }
 484     else
 485     {
 486       Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
 487               .getSelectedItem().toString());
 488     }
 489
 490     /*
 491      * Save Connections settings
 492      */
 493     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 494
 495     jalview.util.BrowserLauncher.resetBrowser();
 496
 497     if (nameLinks.size() > 0)
 498     {
 499       StringBuffer links = new StringBuffer();
 500       sequenceURLLinks = new Vector();
 501       for (int i = 0; i < nameLinks.size(); i++)
 502       {
 503         sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
 504                 + urlLinks.elementAt(i));
 505         links.append(sequenceURLLinks.elementAt(i).toString());
 506         links.append("|");
 507       }
 508       // remove last "|"
 509       links.setLength(links.length() - 1);
 510       Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
 511               links.toString());
 512     }
 513     else
 514     {
 515       Cache.applicationProperties.remove("SEQUENCE_LINKS");
 516     }
 517
 518     Cache.applicationProperties.setProperty("USE_PROXY",
 519             Boolean.toString(useProxy.isSelected()));
 520
 521     Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 522
 523     Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 524
 525     if (useProxy.isSelected())
 526     {
 527       System.setProperty("http.proxyHost", proxyServerTB.getText());
 528       System.setProperty("http.proxyPort", proxyPortTB.getText());
 529     }
 530     else
 531     {
 532       System.setProperty("http.proxyHost", "");
 533       System.setProperty("http.proxyPort", "");
 534     }
 535     Cache.setProperty("VERSION_CHECK",
 536             Boolean.toString(versioncheck.isSelected()));
 537     if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
 538     {
 539       // default is false - we only set this if the user has actively agreed
 540       Cache.setProperty("USAGESTATS",
 541               Boolean.toString(usagestats.isSelected()));
 542     }
 543     if (!questionnaire.isSelected())
 544     {
 545       Cache.setProperty("NOQUESTIONNAIRES", "true");
 546     }
 547     else
 548     {
 549       // special - made easy to edit a property file to disable questionnaires
 550       // by just adding the given line
 551       Cache.removeProperty("NOQUESTIONNAIRES");
 552     }
 553
 554     /*
 555      * Save Output settings
 556      */
 557     Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
 558             Boolean.toString(blcjv.isSelected()));
 559     Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
 560             Boolean.toString(clustaljv.isSelected()));
 561     Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
 562             Boolean.toString(fastajv.isSelected()));
 563     Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
 564             Boolean.toString(msfjv.isSelected()));
 565     Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
 566             Boolean.toString(pfamjv.isSelected()));
 567     Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
 568             Boolean.toString(pileupjv.isSelected()));
 569     Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
 570             Boolean.toString(pirjv.isSelected()));
 571     Cache.applicationProperties.setProperty("PIR_MODELLER",
 572             Boolean.toString(modellerOutput.isSelected()));
 573     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 574
 575     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
 576             Boolean.toString(autoIdWidth.isSelected()));
 577     userIdWidth_actionPerformed();
 578     Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
 579             userIdWidth.getText());
 580
 581     /*
 582      * Save Editing settings
 583      */
 584     Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
 585             Boolean.toString(autoCalculateConsCheck.isSelected()));
 586     Cache.applicationProperties.setProperty("SORT_BY_TREE",
 587             Boolean.toString(sortByTree.isSelected()));
 588     Cache.applicationProperties.setProperty("PAD_GAPS",
 589             Boolean.toString(padGaps.isSelected()));
 590
 591     dasSource.saveProperties(Cache.applicationProperties);
 592     wsPrefs.updateAndRefreshWsMenuConfig(false);
 593     Cache.saveProperties();
 594     Desktop.instance.doConfigureStructurePrefs();
 595     try
 596     {
 597       frame.setClosed(true);
 598     } catch (Exception ex)
 599     {
 600     }
 601   }
 602
 603   /**
 604    * Do any necessary validation before saving settings. Return focus to the
 605    * first tab which fails validation.
 606    *
 607    * @return
 608    */
 609   private boolean validateSettings()
 610   {
 611     if (!validateStructure())
 612     {
 613       structureTab.requestFocusInWindow();
 614       return false;
 615     }
 616     return true;
 617   }
 618
 619   @Override
 620   protected boolean validateStructure()
 621   {
 622     return validateChimeraPath();
 623
 624   }
 625   /**
 626    * DOCUMENT ME!
 627    */
 628   public void startupFileTextfield_mouseClicked()
 629   {
 630     JalviewFileChooser chooser = new JalviewFileChooser(
 631             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 632             new String[]
 633             { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
 634             new String[]
 635             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
 636             jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
 637     chooser.setFileView(new JalviewFileView());
 638     chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
 639
 640     int value = chooser.showOpenDialog(this);
 641
 642     if (value == JalviewFileChooser.APPROVE_OPTION)
 643     {
 644       jalview.bin.Cache.applicationProperties.setProperty(
 645               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
 646       startupFileTextfield.setText(chooser.getSelectedFile()
 647               .getAbsolutePath());
 648     }
 649   }
 650
 651   /**
 652    * DOCUMENT ME!
 653    *
 654    * @param e
 655    *          DOCUMENT ME!
 656    */
 657   public void cancel_actionPerformed(ActionEvent e)
 658   {
 659     try
 660     {
 661       wsPrefs.updateWsMenuConfig(true);
 662       wsPrefs.refreshWs_actionPerformed(e);
 663       frame.setClosed(true);
 664     } catch (Exception ex)
 665     {
 666     }
 667   }
 668
 669   /**
 670    * DOCUMENT ME!
 671    *
 672    * @param e
 673    *          DOCUMENT ME!
 674    */
 675   public void annotations_actionPerformed(ActionEvent e)
 676   {
 677     conservation.setEnabled(annotations.isSelected());
 678     quality.setEnabled(annotations.isSelected());
 679     identity.setEnabled(annotations.isSelected());
 680     showGroupConsensus.setEnabled(annotations.isSelected());
 681     showGroupConservation.setEnabled(annotations.isSelected());
 682     showConsensHistogram.setEnabled(annotations.isSelected()
 683             && (identity.isSelected() || showGroupConsensus.isSelected()));
 684     showConsensLogo.setEnabled(annotations.isSelected()
 685             && (identity.isSelected() || showGroupConsensus.isSelected()));
 686   }
 687
 688   public void newLink_actionPerformed(ActionEvent e)
 689   {
 690
 691     GSequenceLink link = new GSequenceLink();
 692     boolean valid = false;
 693     while (!valid)
 694     {
 695       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 696               MessageManager.getString("label.new_sequence_url_link"),
 697               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 698       {
 699         if (link.checkValid())
 700         {
 701           nameLinks.addElement(link.getName());
 702           urlLinks.addElement(link.getURL());
 703           updateLinkData();
 704           valid = true;
 705         }
 706       }
 707       else
 708       {
 709         break;
 710       }
 711     }
 712   }
 713
 714   public void editLink_actionPerformed(ActionEvent e)
 715   {
 716     GSequenceLink link = new GSequenceLink();
 717
 718     int index = linkNameList.getSelectedIndex();
 719     if (index == -1)
 720     {
 721       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 722               MessageManager.getString("label.no_link_selected"),
 723               MessageManager.getString("label.no_link_selected"),
 724               JOptionPane.WARNING_MESSAGE);
 725       return;
 726     }
 727
 728     link.setName(nameLinks.elementAt(index).toString());
 729     link.setURL(urlLinks.elementAt(index).toString());
 730
 731     boolean valid = false;
 732     while (!valid)
 733     {
 734
 735       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
 736               MessageManager.getString("label.new_sequence_url_link"),
 737               JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
 738       {
 739         if (link.checkValid())
 740         {
 741           nameLinks.setElementAt(link.getName(), index);
 742           urlLinks.setElementAt(link.getURL(), index);
 743           updateLinkData();
 744           valid = true;
 745         }
 746       }
 747
 748       else
 749       {
 750         break;
 751       }
 752     }
 753   }
 754
 755   public void deleteLink_actionPerformed(ActionEvent e)
 756   {
 757     int index = linkNameList.getSelectedIndex();
 758     if (index == -1)
 759     {
 760       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 761               MessageManager.getString("label.no_link_selected"),
 762               MessageManager.getString("label.no_link_selected"),
 763               JOptionPane.WARNING_MESSAGE);
 764       return;
 765     }
 766     nameLinks.removeElementAt(index);
 767     urlLinks.removeElementAt(index);
 768     updateLinkData();
 769   }
 770
 771   void updateLinkData()
 772   {
 773     linkNameList.setListData(nameLinks);
 774     linkURLList.setListData(urlLinks);
 775   }
 776
 777   public void defaultBrowser_mouseClicked(MouseEvent e)
 778   {
 779     JFileChooser chooser = new JFileChooser(".");
 780     chooser.setDialogTitle(MessageManager.getString("label.select_default_browser"));
 781
 782     int value = chooser.showOpenDialog(this);
 783
 784     if (value == JFileChooser.APPROVE_OPTION)
 785     {
 786       defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
 787     }
 788
 789   }
 790
 791   /*
 792    * (non-Javadoc)
 793    *
 794    * @see
 795    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
 796    * .ActionEvent)
 797    */
 798   protected void showunconserved_actionPerformed(ActionEvent e)
 799   {
 800     // TODO Auto-generated method stub
 801     super.showunconserved_actionPerformed(e);
 802   }
 803
 804   public static Collection getGroupURLLinks()
 805   {
 806     return groupURLLinks;
 807   }
 808
 809   @Override
 810   public void minColour_actionPerformed(JPanel panel)
 811   {
 812     Color col = JColorChooser.showDialog(this,
 813             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 814     if (col != null)
 815     {
 816       panel.setBackground(col);
 817     }
 818     panel.repaint();
 819   }
 820
 821   @Override
 822   public void maxColour_actionPerformed(JPanel panel)
 823   {
 824     Color col = JColorChooser.showDialog(this,
 825             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
 826     if (col != null)
 827     {
 828       panel.setBackground(col);
 829     }
 830     panel.repaint();
 831   }
 832
 833   @Override
 834   protected void userIdWidth_actionPerformed()
 835   {
 836     try
 837     {
 838       String val = userIdWidth.getText().trim();
 839       if (val.length() > 0)
 840       {
 841         Integer iw = Integer.parseInt(val);
 842         if (iw.intValue() < 12)
 843         {
 844           throw new NumberFormatException();
 845         }
 846         userIdWidth.setText(iw.toString());
 847       }
 848     } catch (NumberFormatException x)
 849     {
 850       JOptionPane
 851               .showInternalMessageDialog(
 852                       Desktop.desktop,
 853                       MessageManager.getString("warn.user_defined_width_requirements"),
 854                       MessageManager.getString("label.invalid_id_column_width"),
 855                       JOptionPane.WARNING_MESSAGE);
 856       userIdWidth.setText("");
 857     }
 858   }
 859
 860   @Override
 861   protected void autoIdWidth_actionPerformed()
 862   {
 863     userIdWidth.setEnabled(!autoIdWidth.isSelected());
 864     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
 865   }
 866
 867   /**
 868    * Returns true if chimera path is to a valid executable, else show an error
 869    * dialog.
 870    */
 871   private boolean validateChimeraPath()
 872   {
 873     if (chimeraPath.getText().trim().length() > 0)
 874     {
 875       File f = new File(chimeraPath.getText());
 876       if (!f.canExecute())
 877       {
 878         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 879                 MessageManager.getString("label.invalid_chimera_path"),
 880                 MessageManager.getString("label.invalid_name"),
 881                 JOptionPane.ERROR_MESSAGE);
 882         return false;
 883       }
 884     }
 885     return true;
 886   }
 887
 888   /**
 889    * If Chimera is selected, check it can be found on default or user-specified
 890    * path, if not show a warning/help dialog.
 891    */
 892   @Override
 893   protected void structureViewer_actionPerformed(String selectedItem)
 894   {
 895     if (!selectedItem.equals(Viewer.CHIMERA.name()))
 896     {
 897       return;
 898     }
 899     boolean found = false;
 900
 901     /*
 902      * Try user-specified and standard paths for Chimera executable.
 903      */
 904     List<String> paths = StructureManager.getChimeraPaths();
 905     paths.add(0, chimeraPath.getText());
 906     for (String path : paths)
 907     {
 908       if (new File(path.trim()).canExecute())
 909       {
 910         found = true;
 911         break;
 912       }
 913     }
 914     if (!found)
 915     {
 916       String[] options =
 917       { "OK", "Help" };
 918       int showHelp = JOptionPane.showInternalOptionDialog(
 919               Desktop.desktop,
 920               JvSwingUtils.wrapTooltip(true,
 921                       MessageManager.getString("label.chimera_missing")),
 922               "", JOptionPane.YES_NO_OPTION,
 923               JOptionPane.WARNING_MESSAGE, null, options, options[0]);
 924       if (showHelp == JOptionPane.NO_OPTION)
 925       {
 926         try
 927         {
 928           Help.showHelpWindow(HelpId.StructureViewer);
 929         } catch (HelpSetException e)
 930         {
 931           e.printStackTrace();
 932         }
 933       }
 934     }
 935   }
 936
 937 }