2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import jalview.datamodel.PDBEntry;
24 import jalview.structure.StructureImportSettings;
25 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
26 import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
27 import jalview.ws.sifts.SiftsSettings;
29 import java.awt.Color;
30 import java.io.BufferedReader;
32 import java.io.FileInputStream;
33 import java.io.FileOutputStream;
34 import java.io.InputStream;
35 import java.io.InputStreamReader;
36 import java.text.DateFormat;
37 import java.text.SimpleDateFormat;
38 import java.util.Collections;
39 import java.util.Date;
40 import java.util.Enumeration;
41 import java.util.Locale;
42 import java.util.Properties;
43 import java.util.TreeSet;
45 import org.apache.log4j.ConsoleAppender;
46 import org.apache.log4j.Level;
47 import org.apache.log4j.Logger;
48 import org.apache.log4j.SimpleLayout;
51 * Stores and retrieves Jalview Application Properties Lists and fields within
52 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
53 * are alternative values for a tag. <br>
55 * Current properties include:
58 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
59 * logging level for axis (used for web services) <br>
61 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
62 * the logging level for castor (used for serialization) <br>
64 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
66 * <li>SCREEN_WIDTH</li>
67 * <li>SCREEN_HEIGHT</li>
68 * <li>SCREEN_Y=285</li>
69 * <li>SCREEN_X=371</li>
70 * <li>SHOW_FULLSCREEN boolean</li>
71 * <li>FONT_NAME java font name for alignment text display</li>
72 * <li>FONT_SIZE size of displayed alignment text</li>
73 * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
74 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
75 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
76 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
77 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
78 * <li>SHOW_IDENTITY show percentage identity annotation</li>
79 * <li>SHOW_QUALITY show alignment quality annotation</li>
80 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
81 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
82 * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
83 * LABEL_AND_SEQUENCE</li>
84 * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
85 * sequence annotations</li>
86 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
88 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
89 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
90 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
91 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
92 * <li>VERSION the version of the jalview build</li>
93 * <li>BUILD_DATE date of this build</li>
94 * <li>LATEST_VERSION the latest jalview version advertised on the
95 * www.jalview.org</li>
96 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
98 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
100 * <li>RECENT_URL list of recently retrieved URLs</li>
101 * <li>RECENT_FILE list of recently opened files</li>
102 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
103 * <li>PROXY_SERVER the proxy</li>
104 * <li>PROXY_PORT</li>
105 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
107 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
109 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
110 * collecting usage statistics</li>
111 * <li>DAS_LOCAL_SOURCE list of local das sources</li>
112 * <li>SHOW_OVERVIEW boolean for overview window display</li>
113 * <li>ANTI_ALIAS boolean for smooth fonts</li>
114 * <li>RIGHT_ALIGN_IDS boolean</li>
115 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
116 * <li>PAD_GAPS boolean</li>
117 * <li>ID_ITALICS boolean</li>
118 * <li>SHOW_JV_SUFFIX</li>
119 * <li>WRAP_ALIGNMENT</li>
120 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
122 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
123 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
125 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
126 * jalview.utils.GroupURLLink for more info</li>
127 * <li>DAS_REGISTRY_URL the registry to query</li>
128 * <li>DEFAULT_BROWSER for unix</li>
129 * <li>DAS_ACTIVE_SOURCE list of active sources</li>
130 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
132 * <li>VERSION_CHECK (true) check for the latest release version from
133 * www.jalview.org (or the alias given by the www.jalview.org property)</li>
134 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
136 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
138 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
139 * displayed as '.'</li>
140 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
141 * order of a newly displayed tree</li>
142 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
143 * sequence ID strings before attempting retrieval from any datasource</li>
144 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
146 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
147 * in the alignment.</li>
148 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
150 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
152 * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
153 * logo normalised to row height rather than histogram height.</li>
154 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
155 * respond to selections made in other alignments containing the same sequences.
157 * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
158 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
159 * warning dialog box is displayed.</li>
160 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
161 * when shading by annotation</li>
162 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
163 * when shading by annotation</li>
164 * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
165 * requests to be redirected to a mirror of http://www.jalview.org</li>
166 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
167 * alignment figure to accommodate even the longest sequence ID or annotation
169 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
170 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
171 * will override this).</li>
172 * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
174 * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
175 * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
177 * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
179 * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
181 * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
184 * Deprecated settings:
187 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
188 * startup (JWS1 services only)</li>
189 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
190 * (JWS1 services only)</li>
191 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
192 * services in the desktop GUI</li>
193 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
194 * panel in web service preferences</li>
198 * @version $Revision$
203 * property giving log4j level for CASTOR loggers
205 public static final String CASTORLOGLEVEL = "logs.Castor.level";
208 * property giving log4j level for AXIS loggers
210 public static final String AXISLOGLEVEL = "logs.Axis.level";
213 * property giving log4j level for Jalview Log
215 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
217 public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
219 public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
221 public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
223 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
224 .getProperty("user.home")
226 + ".sifts_downloads" + File.separatorChar;
228 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
230 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
233 * Allowed values are PDB or mmCIF
235 private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
238 private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
242 * a date formatter using a fixed (rather than the user's) locale;
243 * this ensures that date properties can be written and re-read successfully
244 * even if the user changes their locale setting
246 private static final DateFormat date_format = SimpleDateFormat
247 .getDateTimeInstance(SimpleDateFormat.MEDIUM,
248 SimpleDateFormat.MEDIUM, Locale.UK);
251 * Initialises the Jalview Application Log
253 public static Logger log;
255 /** Jalview Properties */
256 public static Properties applicationProperties = new Properties()
258 // override results in properties output in alphabetical order
260 public synchronized Enumeration<Object> keys()
262 return Collections.enumeration(new TreeSet<Object>(super.keySet()));
266 /** Default file is ~/.jalview_properties */
267 static String propertiesFile;
269 private static boolean propsAreReadOnly = false;
271 public static void initLogger()
279 // TODO: redirect stdout and stderr here in order to grab the output of
282 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
284 ap.setName("JalviewLogger");
285 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
287 Logger laxis = Logger.getLogger("org.apache.axis");
288 Logger lcastor = Logger.getLogger("org.exolab.castor");
289 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
291 laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
292 Level.INFO.toString())));
293 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
294 Level.INFO.toString())));
295 lcastor = Logger.getLogger("org.exolab.castor.xml");
296 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
297 Level.INFO.toString())));
298 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
299 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
300 // Level.INFO.toString())));
301 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
302 "logs.Jalview.level", Level.INFO.toString())));
303 // laxis.addAppender(ap);
304 // lcastor.addAppender(ap);
305 // jalview.bin.Cache.log.addAppender(ap);
306 // Tell the user that debug is enabled
307 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
308 } catch (Exception ex)
310 System.err.println("Problems initializing the log4j system\n");
311 ex.printStackTrace(System.err);
315 /** Called when Jalview is started */
316 public static void loadProperties(String propsFile)
318 propertiesFile = propsFile;
319 if (propsFile == null)
321 propertiesFile = System.getProperty("user.home") + File.separatorChar
322 + ".jalview_properties";
326 // don't corrupt the file we've been given.
327 propsAreReadOnly = true;
335 fis = new java.net.URL(propertiesFile).openStream();
336 System.out.println("Loading jalview properties from : "
339 .println("Disabling Jalview writing to user's local properties file.");
340 propsAreReadOnly = true;
342 } catch (Exception ex)
348 fis = new FileInputStream(propertiesFile);
350 applicationProperties.load(fis);
352 // remove any old build properties
354 deleteBuildProperties();
356 } catch (Exception ex)
358 System.out.println("Error reading properties file: " + ex);
361 if (getDefault("USE_PROXY", false))
363 String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
364 "PROXY_PORT", "8080");
366 System.out.println("Using proxyServer: " + proxyServer
367 + " proxyPort: " + proxyPort);
369 System.setProperty("http.proxyHost", proxyServer);
370 System.setProperty("http.proxyPort", proxyPort);
373 // LOAD THE AUTHORS FROM THE authors.props file
376 String authorDetails = "jar:".concat(Cache.class
377 .getProtectionDomain().getCodeSource().getLocation()
378 .toString().concat("!/authors.props"));
380 java.net.URL localJarFileURL = new java.net.URL(authorDetails);
382 InputStream in = localJarFileURL.openStream();
383 applicationProperties.load(in);
385 } catch (Exception ex)
387 System.out.println("Error reading author details: " + ex);
388 applicationProperties.remove("AUTHORS");
389 applicationProperties.remove("AUTHORFNAMES");
390 applicationProperties.remove("YEAR");
393 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
394 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
395 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
398 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
399 .getCodeSource().getLocation().toString()
400 .concat("!/.build_properties"));
402 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
404 InputStream in = localJarFileURL.openStream();
405 applicationProperties.load(in);
407 } catch (Exception ex)
409 System.out.println("Error reading build details: " + ex);
410 applicationProperties.remove("VERSION");
413 String jnlpVersion = System.getProperty("jalview.version");
414 String codeVersion = getProperty("VERSION");
415 String codeInstallation = getProperty("INSTALLATION");
416 if (codeVersion == null)
418 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
419 codeVersion = "Test";
420 jnlpVersion = "Test";
421 codeInstallation = "";
425 codeInstallation = " (" + codeInstallation + ")";
427 new BuildDetails(codeVersion, null, codeInstallation);
430 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
432 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
433 "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
435 SiftsSettings.setFailSafePIDThreshold(jalview.bin.Cache.getDefault(
436 "sifts_fail_safe_pid_threshold",
437 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
439 SiftsSettings.setCacheThresholdInDays(jalview.bin.Cache.getDefault(
440 "sifts_cache_threshold_in_days",
441 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
444 .println("Jalview Version: " + codeVersion + codeInstallation);
446 StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
447 .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
448 StructureImportSettings
449 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
450 // StructureImportSettings
451 // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
452 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
453 // jnlpVersion will be null if we're using InstallAnywhere
454 // Dont do this check if running in headless mode
455 if (jnlpVersion == null
456 && getDefault("VERSION_CHECK", true)
457 && (System.getProperty("java.awt.headless") == null || System
458 .getProperty("java.awt.headless").equals("false")))
461 class VersionChecker extends Thread
466 String orgtimeout = System
467 .getProperty("sun.net.client.defaultConnectTimeout");
468 if (orgtimeout == null)
471 System.out.println("# INFO: Setting default net timeout to "
472 + orgtimeout + " seconds.");
474 String remoteVersion = null;
477 System.setProperty("sun.net.client.defaultConnectTimeout",
479 java.net.URL url = new java.net.URL(Cache.getDefault(
480 "www.jalview.org", "http://www.jalview.org")
481 + "/webstart/jalview.jnlp");
482 BufferedReader in = new BufferedReader(new InputStreamReader(
485 while ((line = in.readLine()) != null)
487 if (line.indexOf("jalview.version") == -1)
492 line = line.substring(line.indexOf("value=") + 7);
493 line = line.substring(0, line.lastIndexOf("\""));
494 remoteVersion = line;
497 } catch (Exception ex)
500 .println("Non-fatal exception when checking version at www.jalview.org :");
501 System.out.println(ex);
502 remoteVersion = getProperty("VERSION");
504 System.setProperty("sun.net.client.defaultConnectTimeout",
507 setProperty("LATEST_VERSION", remoteVersion);
511 VersionChecker vc = new VersionChecker();
516 if (jnlpVersion != null)
518 setProperty("LATEST_VERSION", jnlpVersion);
522 applicationProperties.remove("LATEST_VERSION");
526 setProperty("VERSION", codeVersion);
528 // LOAD USERDEFINED COLOURS
529 jalview.gui.UserDefinedColours
530 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
531 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
535 private static void deleteBuildProperties()
537 applicationProperties.remove("LATEST_VERSION");
538 applicationProperties.remove("VERSION");
539 applicationProperties.remove("AUTHORS");
540 applicationProperties.remove("AUTHORFNAMES");
541 applicationProperties.remove("YEAR");
542 applicationProperties.remove("BUILD_DATE");
543 applicationProperties.remove("INSTALLATION");
547 * Gets Jalview application property of given key. Returns null if key not
553 * @return Property value
555 public static String getProperty(String key)
557 return applicationProperties.getProperty(key);
561 * These methods are used when checking if the saved preference is different
562 * to the default setting
565 public static boolean getDefault(String property, boolean def)
567 String string = getProperty(property);
570 def = Boolean.valueOf(string).booleanValue();
577 * These methods are used when checking if the saved preference is different
578 * to the default setting
580 public static String getDefault(String property, String def)
582 String string = getProperty(property);
592 * Stores property in the file "HOME_DIR/.jalview_properties"
597 * String value of property
599 * @return String value of property
601 public static String setProperty(String key, String obj)
606 applicationProperties.setProperty(key, obj);
607 if (!propsAreReadOnly)
609 FileOutputStream out = new FileOutputStream(propertiesFile);
610 applicationProperties.store(out, "---JalviewX Properties File---");
613 } catch (Exception ex)
615 System.out.println("Error setting property: " + key + " " + obj
622 * remove the specified property from the jalview properties file
626 public static void removeProperty(String string)
628 applicationProperties.remove(string);
633 * save the properties to the jalview properties path
635 public static void saveProperties()
637 if (!propsAreReadOnly)
641 FileOutputStream out = new FileOutputStream(propertiesFile);
642 applicationProperties.store(out, "---JalviewX Properties File---");
644 } catch (Exception ex)
646 System.out.println("Error saving properties: " + ex);
652 * internal vamsas class discovery state
654 private static int vamsasJarsArePresent = -1;
657 * Searches for vamsas client classes on class path.
659 * @return true if vamsas client is present on classpath
661 public static boolean vamsasJarsPresent()
663 if (vamsasJarsArePresent == -1)
667 if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
668 "uk.ac.vamsas.client.VorbaId") != null)
670 jalview.bin.Cache.log
671 .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
672 vamsasJarsArePresent = 1;
673 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
674 lvclient.setLevel(Level.toLevel(Cache.getDefault(
675 "logs.Vamsas.Level", Level.INFO.toString())));
677 lvclient.addAppender(log.getAppender("JalviewLogger"));
678 // Tell the user that debug is enabled
679 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
681 } catch (Exception e)
683 vamsasJarsArePresent = 0;
684 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
687 return (vamsasJarsArePresent > 0);
691 * internal vamsas class discovery state
693 private static int groovyJarsArePresent = -1;
696 * Searches for vamsas client classes on class path.
698 * @return true if vamsas client is present on classpath
700 public static boolean groovyJarsPresent()
702 if (groovyJarsArePresent == -1)
706 if (Cache.class.getClassLoader().loadClass(
707 "groovy.lang.GroovyObject") != null)
709 jalview.bin.Cache.log
710 .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
711 groovyJarsArePresent = 1;
712 Logger lgclient = Logger.getLogger("groovy");
713 lgclient.setLevel(Level.toLevel(Cache.getDefault(
714 "logs.Groovy.Level", Level.INFO.toString())));
716 lgclient.addAppender(log.getAppender("JalviewLogger"));
717 // Tell the user that debug is enabled
718 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
722 groovyJarsArePresent = 0;
723 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
724 } catch (Exception e)
726 groovyJarsArePresent = 0;
727 jalview.bin.Cache.log.debug("Groovy Classes are not present");
730 return (groovyJarsArePresent > 0);
734 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
737 protected static Object tracker = null;
739 protected static Class trackerfocus = null;
741 protected static Class jgoogleanalyticstracker = null;
744 * Initialise the google tracker if it is not done already.
746 public static void initGoogleTracker()
750 if (jgoogleanalyticstracker == null)
752 // try to get the tracker class
755 jgoogleanalyticstracker = Cache.class
758 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
759 trackerfocus = Cache.class.getClassLoader().loadClass(
760 "com.boxysystems.jgoogleanalytics.FocusPoint");
761 } catch (Exception e)
763 log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
765 jgoogleanalyticstracker = null;
770 // now initialise tracker
771 Exception re = null, ex = null;
773 String vrs = "No Version Accessible";
776 // Google analytics tracking code for Library Finder
777 tracker = jgoogleanalyticstracker.getConstructor(
778 new Class[] { String.class, String.class, String.class })
782 (vrs = jalview.bin.Cache.getProperty("VERSION")
784 + jalview.bin.Cache.getDefault(
785 "BUILD_DATE", "unknown")),
787 jgoogleanalyticstracker.getMethod("trackAsynchronously",
788 new Class[] { trackerfocus }).invoke(
790 new Object[] { trackerfocus.getConstructor(
791 new Class[] { String.class }).newInstance(
792 new Object[] { "Application Started." }) });
793 } catch (RuntimeException e)
796 } catch (Exception e)
803 if (re != null || ex != null || err != null)
809 log.debug("Caught runtime exception in googletracker init:", re);
814 "Failed to initialise GoogleTracker for Jalview Desktop with version "
820 "Whilst initing GoogleTracker for Jalview Desktop version "
829 .println("Debug: Caught runtime exception in googletracker init:"
831 re.printStackTrace();
836 .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
838 ex.printStackTrace();
844 .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
846 err.printStackTrace();
852 log.debug("Successfully initialised tracker.");
858 * get the user's default colour if available
864 public static Color getDefaultColour(String property, Color defcolour)
866 String colprop = getProperty(property);
871 Color col = jalview.schemes.ColourSchemeProperty
872 .getAWTColorFromName(colprop);
877 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
878 } catch (Exception ex)
880 log.warn("Couldn't parse '" + colprop + "' as a colour for "
885 return (col == null) ? defcolour : col;
889 * store a colour as a Jalview user default property
894 public static void setColourProperty(String property, Color colour)
896 setProperty(property, jalview.util.Format.getHexString(colour));
900 * Stores a formatted date in a jalview property, using a fixed locale.
902 * @param propertyName
904 * @return the formatted date string
906 public static String setDateProperty(String propertyName, Date date)
908 String formatted = date_format.format(date);
909 setProperty(propertyName, formatted);
914 * Reads a date stored in a Jalview property, parses it (using a fixed locale
915 * format) and returns as a Date, or null if parsing fails
917 * @param propertyName
921 public static Date getDateProperty(String propertyName)
923 String val = getProperty(propertyName);
928 return date_format.parse(val);
929 } catch (Exception ex)
931 System.err.println("Invalid or corrupt date in property '"
932 + propertyName + "' : value was '" + val + "'");
939 * get and parse a property as an integer. send any parsing problems to
943 * @return null or Integer
945 public static Integer getIntegerProperty(String property)
947 String val = getProperty(property);
948 if (val != null && (val = val.trim()).length() > 0)
952 return Integer.valueOf(val);
953 } catch (NumberFormatException x)
955 System.err.println("Invalid integer in property '" + property
956 + "' (value was '" + val + "')");
962 private static DasSourceRegistryI sourceRegistry = null;
967 * @return instance of the das source registry
969 public static DasSourceRegistryI getDasSourceRegistry()
971 if (sourceRegistry == null)
973 sourceRegistry = new DasSourceRegistry();
975 return sourceRegistry;
979 * Set the specified value, or remove it if null or empty. Does not save the
985 public static void setOrRemove(String propName, String value)
987 if (propName == null)
991 if (value == null || value.trim().length() < 1)
993 Cache.applicationProperties.remove(propName);
997 Cache.applicationProperties.setProperty(propName, value);