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.DBRefSource;
24 import jalview.structure.StructureViewSettings;
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.Properties;
42 import java.util.TreeSet;
44 import org.apache.log4j.ConsoleAppender;
45 import org.apache.log4j.Level;
46 import org.apache.log4j.Logger;
47 import org.apache.log4j.SimpleLayout;
50 * Stores and retrieves Jalview Application Properties Lists and fields within
51 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
52 * are alternative values for a tag. <br>
54 * Current properties include:
57 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
58 * logging level for axis (used for web services) <br>
60 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
61 * the logging level for castor (used for serialization) <br>
63 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
65 * <li>SCREEN_WIDTH</li>
66 * <li>SCREEN_HEIGHT</li>
67 * <li>SCREEN_Y=285</li>
68 * <li>SCREEN_X=371</li>
69 * <li>SHOW_FULLSCREEN boolean</li>
70 * <li>FONT_NAME java font name for alignment text display</li>
71 * <li>FONT_SIZE size of displayed alignment text</li>
72 * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
73 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
74 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
75 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
76 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
77 * <li>SHOW_IDENTITY show percentage identity annotation</li>
78 * <li>SHOW_QUALITY show alignment quality annotation</li>
79 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
80 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
81 * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
82 * LABEL_AND_SEQUENCE</li>
83 * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
84 * sequence annotations</li>
85 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
87 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
88 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
89 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
90 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
91 * <li>VERSION the version of the jalview build</li>
92 * <li>BUILD_DATE date of this build</li>
93 * <li>LATEST_VERSION the latest jalview version advertised on the
94 * www.jalview.org</li>
95 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
97 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
99 * <li>RECENT_URL list of recently retrieved URLs</li>
100 * <li>RECENT_FILE list of recently opened files</li>
101 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
102 * <li>PROXY_SERVER the proxy</li>
103 * <li>PROXY_PORT</li>
104 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
106 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
108 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
109 * collecting usage statistics</li>
110 * <li>DAS_LOCAL_SOURCE list of local das sources</li>
111 * <li>SHOW_OVERVIEW boolean for overview window display</li>
112 * <li>ANTI_ALIAS boolean for smooth fonts</li>
113 * <li>RIGHT_ALIGN_IDS boolean</li>
114 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
115 * <li>PAD_GAPS boolean</li>
116 * <li>ID_ITALICS boolean</li>
117 * <li>SHOW_JV_SUFFIX</li>
118 * <li>WRAP_ALIGNMENT</li>
119 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
121 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
122 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
124 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
125 * jalview.utils.GroupURLLink for more info</li>
126 * <li>DAS_REGISTRY_URL the registry to query</li>
127 * <li>DEFAULT_BROWSER for unix</li>
128 * <li>DAS_ACTIVE_SOURCE list of active sources</li>
129 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
131 * <li>VERSION_CHECK (true) check for the latest release version from
132 * www.jalview.org (or the alias given by the www.jalview.org property)</li>
133 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
135 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
137 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
138 * displayed as '.'</li>
139 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
140 * order of a newly displayed tree</li>
141 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
142 * sequence ID strings before attempting retrieval from any datasource</li>
143 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
145 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
146 * in the alignment.</li>
147 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
149 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
151 * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
152 * logo normalised to row height rather than histogram height.</li>
153 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
154 * respond to selections made in other alignments containing the same sequences.
156 * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
157 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
158 * warning dialog box is displayed.</li>
159 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
160 * when shading by annotation</li>
161 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
162 * when shading by annotation</li>
163 * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
164 * requests to be redirected to a mirror of http://www.jalview.org</li>
165 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
166 * alignment figure to accommodate even the longest sequence ID or annotation
168 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
169 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
170 * will override this).</li>
171 * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
173 * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
174 * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
176 * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
178 * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
180 * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
183 * Deprecated settings:
186 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
187 * startup (JWS1 services only)</li>
188 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
189 * (JWS1 services only)</li>
190 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
191 * services in the desktop GUI</li>
192 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
193 * panel in web service preferences</li>
197 * @version $Revision$
202 * property giving log4j level for CASTOR loggers
204 public static final String CASTORLOGLEVEL = "logs.Castor.level";
207 * property giving log4j level for AXIS loggers
209 public static final String AXISLOGLEVEL = "logs.Axis.level";
212 * property giving log4j level for Jalview Log
214 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
216 public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
218 public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
220 public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
222 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
223 .getProperty("user.home")
225 + ".sifts_downloads" + File.separatorChar;
227 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
229 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
231 private final static String DEFAULT_STRUCTURE_FORMAT = DBRefSource.PDB;
234 * Initialises the Jalview Application Log
236 public static Logger log;
238 /** Jalview Properties */
239 public static Properties applicationProperties = new Properties()
241 // override results in properties output in alphabetical order
243 public synchronized Enumeration<Object> keys()
245 return Collections.enumeration(new TreeSet<Object>(super.keySet()));
249 /** Default file is ~/.jalview_properties */
250 static String propertiesFile;
252 private static boolean propsAreReadOnly = false;
254 public static void initLogger()
262 // TODO: redirect stdout and stderr here in order to grab the output of
265 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
267 ap.setName("JalviewLogger");
268 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
270 Logger laxis = Logger.getLogger("org.apache.axis");
271 Logger lcastor = Logger.getLogger("org.exolab.castor");
272 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
274 laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
275 Level.INFO.toString())));
276 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
277 Level.INFO.toString())));
278 lcastor = Logger.getLogger("org.exolab.castor.xml");
279 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
280 Level.INFO.toString())));
281 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
282 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
283 // Level.INFO.toString())));
284 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
285 "logs.Jalview.level", Level.INFO.toString())));
286 // laxis.addAppender(ap);
287 // lcastor.addAppender(ap);
288 // jalview.bin.Cache.log.addAppender(ap);
289 // Tell the user that debug is enabled
290 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
291 } catch (Exception ex)
293 System.err.println("Problems initializing the log4j system\n");
294 ex.printStackTrace(System.err);
298 /** Called when Jalview is started */
299 public static void loadProperties(String propsFile)
301 propertiesFile = propsFile;
302 if (propsFile == null)
304 propertiesFile = System.getProperty("user.home") + File.separatorChar
305 + ".jalview_properties";
309 // don't corrupt the file we've been given.
310 propsAreReadOnly = true;
318 fis = new java.net.URL(propertiesFile).openStream();
319 System.out.println("Loading jalview properties from : "
322 .println("Disabling Jalview writing to user's local properties file.");
323 propsAreReadOnly = true;
325 } catch (Exception ex)
331 fis = new FileInputStream(propertiesFile);
333 applicationProperties.load(fis);
335 // remove any old build properties
337 deleteBuildProperties();
339 } catch (Exception ex)
341 System.out.println("Error reading properties file: " + ex);
344 if (getDefault("USE_PROXY", false))
346 String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
347 "PROXY_PORT", "8080");
349 System.out.println("Using proxyServer: " + proxyServer
350 + " proxyPort: " + proxyPort);
352 System.setProperty("http.proxyHost", proxyServer);
353 System.setProperty("http.proxyPort", proxyPort);
356 // LOAD THE AUTHORS FROM THE authors.props file
359 String authorDetails = "jar:".concat(Cache.class
360 .getProtectionDomain().getCodeSource().getLocation()
361 .toString().concat("!/authors.props"));
363 java.net.URL localJarFileURL = new java.net.URL(authorDetails);
365 InputStream in = localJarFileURL.openStream();
366 applicationProperties.load(in);
368 } catch (Exception ex)
370 System.out.println("Error reading author details: " + ex);
371 applicationProperties.remove("AUTHORS");
372 applicationProperties.remove("AUTHORFNAMES");
373 applicationProperties.remove("YEAR");
376 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
377 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
378 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
381 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
382 .getCodeSource().getLocation().toString()
383 .concat("!/.build_properties"));
385 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
387 InputStream in = localJarFileURL.openStream();
388 applicationProperties.load(in);
390 } catch (Exception ex)
392 System.out.println("Error reading build details: " + ex);
393 applicationProperties.remove("VERSION");
396 String jnlpVersion = System.getProperty("jalview.version");
397 String codeVersion = getProperty("VERSION");
398 String codeInstallation = getProperty("INSTALLATION");
399 if (codeVersion == null)
401 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
402 codeVersion = "Test";
403 jnlpVersion = "Test";
404 codeInstallation = "";
408 codeInstallation = " (" + codeInstallation + ")";
410 new BuildDetails(codeVersion, null, codeInstallation);
413 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
415 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
416 "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
418 SiftsSettings.setFailSafePIDThreshold(jalview.bin.Cache.getDefault(
419 "sifts_fail_safe_pid_threshold",
420 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
422 SiftsSettings.setCacheThresholdInDays(jalview.bin.Cache.getDefault(
423 "sifts_cache_threshold_in_days",
424 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
427 .println("Jalview Version: " + codeVersion + codeInstallation);
429 StructureViewSettings.setCurrentDefaultFormat(jalview.bin.Cache
431 "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
432 // jnlpVersion will be null if we're using InstallAnywhere
433 // Dont do this check if running in headless mode
434 if (jnlpVersion == null
435 && getDefault("VERSION_CHECK", true)
436 && (System.getProperty("java.awt.headless") == null || System
437 .getProperty("java.awt.headless").equals("false")))
440 class VersionChecker extends Thread
445 String orgtimeout = System
446 .getProperty("sun.net.client.defaultConnectTimeout");
447 if (orgtimeout == null)
450 System.out.println("# INFO: Setting default net timeout to "
451 + orgtimeout + " seconds.");
453 String remoteVersion = null;
456 System.setProperty("sun.net.client.defaultConnectTimeout",
458 java.net.URL url = new java.net.URL(Cache.getDefault(
459 "www.jalview.org", "http://www.jalview.org")
460 + "/webstart/jalview.jnlp");
461 BufferedReader in = new BufferedReader(new InputStreamReader(
464 while ((line = in.readLine()) != null)
466 if (line.indexOf("jalview.version") == -1)
471 line = line.substring(line.indexOf("value=") + 7);
472 line = line.substring(0, line.lastIndexOf("\""));
473 remoteVersion = line;
476 } catch (Exception ex)
479 .println("Non-fatal exception when checking version at www.jalview.org :");
480 System.out.println(ex);
481 remoteVersion = getProperty("VERSION");
483 System.setProperty("sun.net.client.defaultConnectTimeout",
486 setProperty("LATEST_VERSION", remoteVersion);
490 VersionChecker vc = new VersionChecker();
495 if (jnlpVersion != null)
497 setProperty("LATEST_VERSION", jnlpVersion);
501 applicationProperties.remove("LATEST_VERSION");
505 setProperty("VERSION", codeVersion);
507 // LOAD USERDEFINED COLOURS
508 jalview.gui.UserDefinedColours
509 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
510 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
514 private static void deleteBuildProperties()
516 applicationProperties.remove("LATEST_VERSION");
517 applicationProperties.remove("VERSION");
518 applicationProperties.remove("AUTHORS");
519 applicationProperties.remove("AUTHORFNAMES");
520 applicationProperties.remove("YEAR");
521 applicationProperties.remove("BUILD_DATE");
522 applicationProperties.remove("INSTALLATION");
526 * Gets Jalview application property of given key. Returns null if key not
532 * @return Property value
534 public static String getProperty(String key)
536 return applicationProperties.getProperty(key);
540 * These methods are used when checking if the saved preference is different
541 * to the default setting
544 public static boolean getDefault(String property, boolean def)
546 String string = getProperty(property);
549 def = Boolean.valueOf(string).booleanValue();
556 * These methods are used when checking if the saved preference is different
557 * to the default setting
559 public static String getDefault(String property, String def)
561 String string = getProperty(property);
571 * Stores property in the file "HOME_DIR/.jalview_properties"
576 * String value of property
578 * @return String value of property
580 public static String setProperty(String key, String obj)
585 applicationProperties.setProperty(key, obj);
586 if (!propsAreReadOnly)
588 FileOutputStream out = new FileOutputStream(propertiesFile);
589 applicationProperties.store(out, "---JalviewX Properties File---");
592 } catch (Exception ex)
594 System.out.println("Error setting property: " + key + " " + obj
601 * remove the specified property from the jalview properties file
605 public static void removeProperty(String string)
607 applicationProperties.remove(string);
612 * save the properties to the jalview properties path
614 public static void saveProperties()
616 if (!propsAreReadOnly)
620 FileOutputStream out = new FileOutputStream(propertiesFile);
621 applicationProperties.store(out, "---JalviewX Properties File---");
623 } catch (Exception ex)
625 System.out.println("Error saving properties: " + ex);
631 * internal vamsas class discovery state
633 private static int vamsasJarsArePresent = -1;
636 * Searches for vamsas client classes on class path.
638 * @return true if vamsas client is present on classpath
640 public static boolean vamsasJarsPresent()
642 if (vamsasJarsArePresent == -1)
646 if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
647 "uk.ac.vamsas.client.VorbaId") != null)
649 jalview.bin.Cache.log
650 .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
651 vamsasJarsArePresent = 1;
652 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
653 lvclient.setLevel(Level.toLevel(Cache.getDefault(
654 "logs.Vamsas.Level", Level.INFO.toString())));
656 lvclient.addAppender(log.getAppender("JalviewLogger"));
657 // Tell the user that debug is enabled
658 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
660 } catch (Exception e)
662 vamsasJarsArePresent = 0;
663 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
666 return (vamsasJarsArePresent > 0);
670 * internal vamsas class discovery state
672 private static int groovyJarsArePresent = -1;
675 * Searches for vamsas client classes on class path.
677 * @return true if vamsas client is present on classpath
679 public static boolean groovyJarsPresent()
681 if (groovyJarsArePresent == -1)
685 if (Cache.class.getClassLoader().loadClass(
686 "groovy.lang.GroovyObject") != null)
688 jalview.bin.Cache.log
689 .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
690 groovyJarsArePresent = 1;
691 Logger lgclient = Logger.getLogger("groovy");
692 lgclient.setLevel(Level.toLevel(Cache.getDefault(
693 "logs.Groovy.Level", Level.INFO.toString())));
695 lgclient.addAppender(log.getAppender("JalviewLogger"));
696 // Tell the user that debug is enabled
697 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
701 groovyJarsArePresent = 0;
702 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
703 } catch (Exception e)
705 groovyJarsArePresent = 0;
706 jalview.bin.Cache.log.debug("Groovy Classes are not present");
709 return (groovyJarsArePresent > 0);
713 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
716 protected static Object tracker = null;
718 protected static Class trackerfocus = null;
720 protected static Class jgoogleanalyticstracker = null;
723 * Initialise the google tracker if it is not done already.
725 public static void initGoogleTracker()
729 if (jgoogleanalyticstracker == null)
731 // try to get the tracker class
734 jgoogleanalyticstracker = Cache.class
737 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
738 trackerfocus = Cache.class.getClassLoader().loadClass(
739 "com.boxysystems.jgoogleanalytics.FocusPoint");
740 } catch (Exception e)
742 log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
744 jgoogleanalyticstracker = null;
749 // now initialise tracker
750 Exception re = null, ex = null;
752 String vrs = "No Version Accessible";
755 // Google analytics tracking code for Library Finder
756 tracker = jgoogleanalyticstracker.getConstructor(
757 new Class[] { String.class, String.class, String.class })
761 (vrs = jalview.bin.Cache.getProperty("VERSION")
763 + jalview.bin.Cache.getDefault(
764 "BUILD_DATE", "unknown")),
766 jgoogleanalyticstracker.getMethod("trackAsynchronously",
767 new Class[] { trackerfocus }).invoke(
769 new Object[] { trackerfocus.getConstructor(
770 new Class[] { String.class }).newInstance(
771 new Object[] { "Application Started." }) });
772 } catch (RuntimeException e)
775 } catch (Exception e)
782 if (re != null || ex != null || err != null)
788 log.debug("Caught runtime exception in googletracker init:", re);
793 "Failed to initialise GoogleTracker for Jalview Desktop with version "
799 "Whilst initing GoogleTracker for Jalview Desktop version "
808 .println("Debug: Caught runtime exception in googletracker init:"
810 re.printStackTrace();
815 .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
817 ex.printStackTrace();
823 .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
825 err.printStackTrace();
831 log.debug("Successfully initialised tracker.");
837 * get the user's default colour if available
843 public static Color getDefaultColour(String property, Color defcolour)
845 String colprop = getProperty(property);
850 Color col = jalview.schemes.ColourSchemeProperty
851 .getAWTColorFromName(colprop);
856 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
857 } catch (Exception ex)
859 log.warn("Couldn't parse '" + colprop + "' as a colour for "
864 return (col == null) ? defcolour : col;
868 * store a colour as a Jalview user default property
873 public static void setColourProperty(String property, Color colour)
875 setProperty(property, jalview.util.Format.getHexString(colour));
878 public static final DateFormat date_format = SimpleDateFormat
879 .getDateTimeInstance();
882 * store a date in a jalview property
887 public static void setDateProperty(String property, Date time)
889 setProperty(property, date_format.format(time));
893 * read a date stored in a jalview property
896 * @return valid date as stored by setDateProperty, or null
899 public static Date getDateProperty(String property)
901 String val = getProperty(property);
906 return date_format.parse(val);
907 } catch (Exception ex)
909 System.err.println("Invalid or corrupt date in property '"
910 + property + "' : value was '" + val + "'");
917 * get and parse a property as an integer. send any parsing problems to
921 * @return null or Integer
923 public static Integer getIntegerProperty(String property)
925 String val = getProperty(property);
926 if (val != null && (val = val.trim()).length() > 0)
930 return Integer.valueOf(val);
931 } catch (NumberFormatException x)
933 System.err.println("Invalid integer in property '" + property
934 + "' (value was '" + val + "')");
940 private static DasSourceRegistryI sourceRegistry = null;
945 * @return instance of the das source registry
947 public static DasSourceRegistryI getDasSourceRegistry()
949 if (sourceRegistry == null)
951 sourceRegistry = new DasSourceRegistry();
953 return sourceRegistry;
957 * Set the specified value, or remove it if null or empty. Does not save the
963 public static void setOrRemove(String propName, String value)
965 if (propName == null)
969 if (value == null || value.trim().length() < 1)
971 Cache.applicationProperties.remove(propName);
975 Cache.applicationProperties.setProperty(propName, value);