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.ws.dbsources.das.api.DasSourceRegistryI;
24 import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
25 import jalview.ws.sifts.SiftsSettings;
27 import java.awt.Color;
28 import java.io.BufferedReader;
30 import java.io.FileInputStream;
31 import java.io.FileOutputStream;
32 import java.io.InputStream;
33 import java.io.InputStreamReader;
34 import java.text.DateFormat;
35 import java.text.SimpleDateFormat;
36 import java.util.Collections;
37 import java.util.Date;
38 import java.util.Enumeration;
39 import java.util.Properties;
40 import java.util.TreeSet;
42 import org.apache.log4j.ConsoleAppender;
43 import org.apache.log4j.Level;
44 import org.apache.log4j.Logger;
45 import org.apache.log4j.SimpleLayout;
48 * Stores and retrieves Jalview Application Properties Lists and fields within
49 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
50 * are alternative values for a tag. <br>
52 * Current properties include:
55 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
56 * logging level for axis (used for web services) <br>
58 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
59 * the logging level for castor (used for serialization) <br>
61 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
63 * <li>SCREEN_WIDTH</li>
64 * <li>SCREEN_HEIGHT</li>
65 * <li>SCREEN_Y=285</li>
66 * <li>SCREEN_X=371</li>
67 * <li>SHOW_FULLSCREEN boolean</li>
68 * <li>FONT_NAME java font name for alignment text display</li>
69 * <li>FONT_SIZE size of displayed alignment text</li>
70 * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
71 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
72 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
73 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
74 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
75 * <li>SHOW_IDENTITY show percentage identity annotation</li>
76 * <li>SHOW_QUALITY show alignment quality annotation</li>
77 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
78 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
79 * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
80 * LABEL_AND_SEQUENCE</li>
81 * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
82 * sequence annotations</li>
83 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
85 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
86 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
87 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
88 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
89 * <li>VERSION the version of the jalview build</li>
90 * <li>BUILD_DATE date of this build</li>
91 * <li>LATEST_VERSION the latest jalview version advertised on the
92 * www.jalview.org</li>
93 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
95 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
97 * <li>RECENT_URL list of recently retrieved URLs</li>
98 * <li>RECENT_FILE list of recently opened files</li>
99 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
100 * <li>PROXY_SERVER the proxy</li>
101 * <li>PROXY_PORT</li>
102 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
104 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
106 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
107 * collecting usage statistics</li>
108 * <li>DAS_LOCAL_SOURCE list of local das sources</li>
109 * <li>SHOW_OVERVIEW boolean for overview window display</li>
110 * <li>ANTI_ALIAS boolean for smooth fonts</li>
111 * <li>RIGHT_ALIGN_IDS boolean</li>
112 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
113 * <li>PAD_GAPS boolean</li>
114 * <li>ID_ITALICS boolean</li>
115 * <li>SHOW_JV_SUFFIX</li>
116 * <li>WRAP_ALIGNMENT</li>
117 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
119 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
120 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
122 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
123 * jalview.utils.GroupURLLink for more info</li>
124 * <li>DAS_REGISTRY_URL the registry to query</li>
125 * <li>DEFAULT_BROWSER for unix</li>
126 * <li>DAS_ACTIVE_SOURCE list of active sources</li>
127 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
129 * <li>VERSION_CHECK (true) check for the latest release version from
130 * www.jalview.org (or the alias given by the www.jalview.org property)</li>
131 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
133 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
135 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
136 * displayed as '.'</li>
137 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
138 * order of a newly displayed tree</li>
139 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
140 * sequence ID strings before attempting retrieval from any datasource</li>
141 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
143 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
144 * in the alignment.</li>
145 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
147 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
149 * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
150 * logo normalised to row height rather than histogram height.</li>
151 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
152 * respond to selections made in other alignments containing the same sequences.
154 * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
155 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
156 * warning dialog box is displayed.</li>
157 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
158 * when shading by annotation</li>
159 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
160 * when shading by annotation</li>
161 * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
162 * requests to be redirected to a mirror of http://www.jalview.org</li>
163 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
164 * alignment figure to accommodate even the longest sequence ID or annotation
166 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
167 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
168 * will override this).</li>
169 * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
171 * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
172 * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
174 * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
176 * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
178 * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
181 * Deprecated settings:
184 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
185 * startup (JWS1 services only)</li>
186 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
187 * (JWS1 services only)</li>
188 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
189 * services in the desktop GUI</li>
190 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
191 * panel in web service preferences</li>
195 * @version $Revision$
200 * property giving log4j level for CASTOR loggers
202 public static final String CASTORLOGLEVEL = "logs.Castor.level";
205 * property giving log4j level for AXIS loggers
207 public static final String AXISLOGLEVEL = "logs.Axis.level";
210 * property giving log4j level for Jalview Log
212 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
214 public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
216 public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
218 public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
220 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
221 .getProperty("user.home")
223 + ".sifts_downloads" + File.separatorChar;
225 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
227 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
230 * Initialises the Jalview Application Log
232 public static Logger log;
234 /** Jalview Properties */
235 public static Properties applicationProperties = new Properties()
237 // override results in properties output in alphabetical order
239 public synchronized Enumeration<Object> keys()
241 return Collections.enumeration(new TreeSet<Object>(super.keySet()));
245 /** Default file is ~/.jalview_properties */
246 static String propertiesFile;
248 private static boolean propsAreReadOnly = false;
250 public static void initLogger()
258 // TODO: redirect stdout and stderr here in order to grab the output of
261 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
263 ap.setName("JalviewLogger");
264 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
266 Logger laxis = Logger.getLogger("org.apache.axis");
267 Logger lcastor = Logger.getLogger("org.exolab.castor");
268 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
270 laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
271 Level.INFO.toString())));
272 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
273 Level.INFO.toString())));
274 lcastor = Logger.getLogger("org.exolab.castor.xml");
275 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
276 Level.INFO.toString())));
277 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
278 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
279 // Level.INFO.toString())));
280 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
281 "logs.Jalview.level", Level.INFO.toString())));
282 // laxis.addAppender(ap);
283 // lcastor.addAppender(ap);
284 // jalview.bin.Cache.log.addAppender(ap);
285 // Tell the user that debug is enabled
286 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
287 } catch (Exception ex)
289 System.err.println("Problems initializing the log4j system\n");
290 ex.printStackTrace(System.err);
294 /** Called when Jalview is started */
295 public static void loadProperties(String propsFile)
297 propertiesFile = propsFile;
298 if (propsFile == null)
300 propertiesFile = System.getProperty("user.home") + File.separatorChar
301 + ".jalview_properties";
305 // don't corrupt the file we've been given.
306 propsAreReadOnly = true;
314 fis = new java.net.URL(propertiesFile).openStream();
315 System.out.println("Loading jalview properties from : "
318 .println("Disabling Jalview writing to user's local properties file.");
319 propsAreReadOnly = true;
321 } catch (Exception ex)
327 fis = new FileInputStream(propertiesFile);
329 applicationProperties.load(fis);
331 // remove any old build properties
333 deleteBuildProperties();
335 } catch (Exception ex)
337 System.out.println("Error reading properties file: " + ex);
340 if (getDefault("USE_PROXY", false))
342 String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
343 "PROXY_PORT", "8080");
345 System.out.println("Using proxyServer: " + proxyServer
346 + " proxyPort: " + proxyPort);
348 System.setProperty("http.proxyHost", proxyServer);
349 System.setProperty("http.proxyPort", proxyPort);
352 // LOAD THE AUTHORS FROM THE authors.props file
355 String authorDetails = "jar:".concat(Cache.class
356 .getProtectionDomain().getCodeSource().getLocation()
357 .toString().concat("!/authors.props"));
359 java.net.URL localJarFileURL = new java.net.URL(authorDetails);
361 InputStream in = localJarFileURL.openStream();
362 applicationProperties.load(in);
364 } catch (Exception ex)
366 System.out.println("Error reading author details: " + ex);
367 applicationProperties.remove("AUTHORS");
368 applicationProperties.remove("AUTHORFNAMES");
369 applicationProperties.remove("YEAR");
372 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
373 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
374 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
377 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
378 .getCodeSource().getLocation().toString()
379 .concat("!/.build_properties"));
381 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
383 InputStream in = localJarFileURL.openStream();
384 applicationProperties.load(in);
386 } catch (Exception ex)
388 System.out.println("Error reading build details: " + ex);
389 applicationProperties.remove("VERSION");
392 String jnlpVersion = System.getProperty("jalview.version");
393 String codeVersion = getProperty("VERSION");
394 String codeInstallation = getProperty("INSTALLATION");
395 if (codeVersion == null)
397 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
398 codeVersion = "Test";
399 jnlpVersion = "Test";
400 codeInstallation = "";
404 codeInstallation = " (" + codeInstallation + ")";
406 new BuildDetails(codeVersion, null, codeInstallation);
409 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
411 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
412 "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
414 SiftsSettings.setFailSafePIDThreshold(jalview.bin.Cache.getDefault(
415 "sifts_fail_safe_pid_threshold",
416 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
418 SiftsSettings.setCacheThresholdInDays(jalview.bin.Cache.getDefault(
419 "sifts_cache_threshold_in_days",
420 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
423 .println("Jalview Version: " + codeVersion + codeInstallation);
425 // jnlpVersion will be null if we're using InstallAnywhere
426 // Dont do this check if running in headless mode
427 if (jnlpVersion == null
428 && getDefault("VERSION_CHECK", true)
429 && (System.getProperty("java.awt.headless") == null || System
430 .getProperty("java.awt.headless").equals("false")))
433 class VersionChecker extends Thread
438 String orgtimeout = System
439 .getProperty("sun.net.client.defaultConnectTimeout");
440 if (orgtimeout == null)
443 System.out.println("# INFO: Setting default net timeout to "
444 + orgtimeout + " seconds.");
446 String remoteVersion = null;
449 System.setProperty("sun.net.client.defaultConnectTimeout",
451 java.net.URL url = new java.net.URL(Cache.getDefault(
452 "www.jalview.org", "http://www.jalview.org")
453 + "/webstart/jalview.jnlp");
454 BufferedReader in = new BufferedReader(new InputStreamReader(
457 while ((line = in.readLine()) != null)
459 if (line.indexOf("jalview.version") == -1)
464 line = line.substring(line.indexOf("value=") + 7);
465 line = line.substring(0, line.lastIndexOf("\""));
466 remoteVersion = line;
469 } catch (Exception ex)
472 .println("Non-fatal exception when checking version at www.jalview.org :");
473 System.out.println(ex);
474 remoteVersion = getProperty("VERSION");
476 System.setProperty("sun.net.client.defaultConnectTimeout",
479 setProperty("LATEST_VERSION", remoteVersion);
483 VersionChecker vc = new VersionChecker();
488 if (jnlpVersion != null)
490 setProperty("LATEST_VERSION", jnlpVersion);
494 applicationProperties.remove("LATEST_VERSION");
498 setProperty("VERSION", codeVersion);
500 // LOAD USERDEFINED COLOURS
501 jalview.gui.UserDefinedColours
502 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
503 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
507 private static void deleteBuildProperties()
509 applicationProperties.remove("LATEST_VERSION");
510 applicationProperties.remove("VERSION");
511 applicationProperties.remove("AUTHORS");
512 applicationProperties.remove("AUTHORFNAMES");
513 applicationProperties.remove("YEAR");
514 applicationProperties.remove("BUILD_DATE");
515 applicationProperties.remove("INSTALLATION");
519 * Gets Jalview application property of given key. Returns null if key not
525 * @return Property value
527 public static String getProperty(String key)
529 return applicationProperties.getProperty(key);
533 * These methods are used when checking if the saved preference is different
534 * to the default setting
537 public static boolean getDefault(String property, boolean def)
539 String string = getProperty(property);
542 def = Boolean.valueOf(string).booleanValue();
549 * These methods are used when checking if the saved preference is different
550 * to the default setting
552 public static String getDefault(String property, String def)
554 String string = getProperty(property);
564 * Stores property in the file "HOME_DIR/.jalview_properties"
569 * String value of property
571 * @return String value of property
573 public static String setProperty(String key, String obj)
578 applicationProperties.setProperty(key, obj);
579 if (!propsAreReadOnly)
581 FileOutputStream out = new FileOutputStream(propertiesFile);
582 applicationProperties.store(out, "---JalviewX Properties File---");
585 } catch (Exception ex)
587 System.out.println("Error setting property: " + key + " " + obj
594 * remove the specified property from the jalview properties file
598 public static void removeProperty(String string)
600 applicationProperties.remove(string);
605 * save the properties to the jalview properties path
607 public static void saveProperties()
609 if (!propsAreReadOnly)
613 FileOutputStream out = new FileOutputStream(propertiesFile);
614 applicationProperties.store(out, "---JalviewX Properties File---");
616 } catch (Exception ex)
618 System.out.println("Error saving properties: " + ex);
624 * internal vamsas class discovery state
626 private static int vamsasJarsArePresent = -1;
629 * Searches for vamsas client classes on class path.
631 * @return true if vamsas client is present on classpath
633 public static boolean vamsasJarsPresent()
635 if (vamsasJarsArePresent == -1)
639 if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
640 "uk.ac.vamsas.client.VorbaId") != null)
642 jalview.bin.Cache.log
643 .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
644 vamsasJarsArePresent = 1;
645 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
646 lvclient.setLevel(Level.toLevel(Cache.getDefault(
647 "logs.Vamsas.Level", Level.INFO.toString())));
649 lvclient.addAppender(log.getAppender("JalviewLogger"));
650 // Tell the user that debug is enabled
651 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
653 } catch (Exception e)
655 vamsasJarsArePresent = 0;
656 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
659 return (vamsasJarsArePresent > 0);
663 * internal vamsas class discovery state
665 private static int groovyJarsArePresent = -1;
668 * Searches for vamsas client classes on class path.
670 * @return true if vamsas client is present on classpath
672 public static boolean groovyJarsPresent()
674 if (groovyJarsArePresent == -1)
678 if (Cache.class.getClassLoader().loadClass(
679 "groovy.lang.GroovyObject") != null)
681 jalview.bin.Cache.log
682 .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
683 groovyJarsArePresent = 1;
684 Logger lgclient = Logger.getLogger("groovy");
685 lgclient.setLevel(Level.toLevel(Cache.getDefault(
686 "logs.Groovy.Level", Level.INFO.toString())));
688 lgclient.addAppender(log.getAppender("JalviewLogger"));
689 // Tell the user that debug is enabled
690 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
694 groovyJarsArePresent = 0;
695 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
696 } catch (Exception e)
698 groovyJarsArePresent = 0;
699 jalview.bin.Cache.log.debug("Groovy Classes are not present");
702 return (groovyJarsArePresent > 0);
706 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
709 protected static Object tracker = null;
711 protected static Class trackerfocus = null;
713 protected static Class jgoogleanalyticstracker = null;
716 * Initialise the google tracker if it is not done already.
718 public static void initGoogleTracker()
722 if (jgoogleanalyticstracker == null)
724 // try to get the tracker class
727 jgoogleanalyticstracker = Cache.class
730 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
731 trackerfocus = Cache.class.getClassLoader().loadClass(
732 "com.boxysystems.jgoogleanalytics.FocusPoint");
733 } catch (Exception e)
735 log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
737 jgoogleanalyticstracker = null;
742 // now initialise tracker
743 Exception re = null, ex = null;
745 String vrs = "No Version Accessible";
748 // Google analytics tracking code for Library Finder
749 tracker = jgoogleanalyticstracker.getConstructor(
750 new Class[] { String.class, String.class, String.class })
754 (vrs = jalview.bin.Cache.getProperty("VERSION")
756 + jalview.bin.Cache.getDefault(
757 "BUILD_DATE", "unknown")),
759 jgoogleanalyticstracker.getMethod("trackAsynchronously",
760 new Class[] { trackerfocus }).invoke(
762 new Object[] { trackerfocus.getConstructor(
763 new Class[] { String.class }).newInstance(
764 new Object[] { "Application Started." }) });
765 } catch (RuntimeException e)
768 } catch (Exception e)
775 if (re != null || ex != null || err != null)
781 log.debug("Caught runtime exception in googletracker init:", re);
786 "Failed to initialise GoogleTracker for Jalview Desktop with version "
792 "Whilst initing GoogleTracker for Jalview Desktop version "
801 .println("Debug: Caught runtime exception in googletracker init:"
803 re.printStackTrace();
808 .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
810 ex.printStackTrace();
816 .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
818 err.printStackTrace();
824 log.debug("Successfully initialised tracker.");
830 * get the user's default colour if available
836 public static Color getDefaultColour(String property, Color defcolour)
838 String colprop = getProperty(property);
843 Color col = jalview.schemes.ColourSchemeProperty
844 .getAWTColorFromName(colprop);
849 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
850 } catch (Exception ex)
852 log.warn("Couldn't parse '" + colprop + "' as a colour for "
857 return (col == null) ? defcolour : col;
861 * store a colour as a Jalview user default property
866 public static void setColourProperty(String property, Color colour)
868 setProperty(property, jalview.util.Format.getHexString(colour));
871 public static final DateFormat date_format = SimpleDateFormat
872 .getDateTimeInstance();
875 * store a date in a jalview property
880 public static void setDateProperty(String property, Date time)
882 setProperty(property, date_format.format(time));
886 * read a date stored in a jalview property
889 * @return valid date as stored by setDateProperty, or null
892 public static Date getDateProperty(String property)
894 String val = getProperty(property);
899 return date_format.parse(val);
900 } catch (Exception ex)
902 System.err.println("Invalid or corrupt date in property '"
903 + property + "' : value was '" + val + "'");
910 * get and parse a property as an integer. send any parsing problems to
914 * @return null or Integer
916 public static Integer getIntegerProperty(String property)
918 String val = getProperty(property);
919 if (val != null && (val = val.trim()).length() > 0)
923 return Integer.valueOf(val);
924 } catch (NumberFormatException x)
926 System.err.println("Invalid integer in property '" + property
927 + "' (value was '" + val + "')");
933 private static DasSourceRegistryI sourceRegistry = null;
938 * @return instance of the das source registry
940 public static DasSourceRegistryI getDasSourceRegistry()
942 if (sourceRegistry == null)
944 sourceRegistry = new DasSourceRegistry();
946 return sourceRegistry;
950 * Set the specified value, or remove it if null or empty. Does not save the
956 public static void setOrRemove(String propName, String value)
958 if (propName == null)
962 if (value == null || value.trim().length() < 1)
964 Cache.applicationProperties.remove(propName);
968 Cache.applicationProperties.setProperty(propName, value);