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