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.urls.IdOrgSettings;
26 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
27 import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
28 import jalview.ws.sifts.SiftsSettings;
30 import java.awt.Color;
31 import java.io.BufferedReader;
33 import java.io.FileInputStream;
34 import java.io.FileOutputStream;
35 import java.io.InputStream;
36 import java.io.InputStreamReader;
37 import java.text.DateFormat;
38 import java.text.SimpleDateFormat;
39 import java.util.Collections;
40 import java.util.Date;
41 import java.util.Enumeration;
42 import java.util.Locale;
43 import java.util.Properties;
44 import java.util.TreeSet;
46 import org.apache.log4j.ConsoleAppender;
47 import org.apache.log4j.Level;
48 import org.apache.log4j.Logger;
49 import org.apache.log4j.SimpleLayout;
52 * Stores and retrieves Jalview Application Properties Lists and fields within
53 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
54 * are alternative values for a tag. <br>
56 * Current properties include:
59 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
60 * logging level for axis (used for web services) <br>
62 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
63 * the logging level for castor (used for serialization) <br>
65 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
67 * <li>SCREEN_WIDTH</li>
68 * <li>SCREEN_HEIGHT</li>
69 * <li>SCREEN_Y=285</li>
70 * <li>SCREEN_X=371</li>
71 * <li>SHOW_FULLSCREEN boolean</li>
72 * <li>FONT_NAME java font name for alignment text display</li>
73 * <li>FONT_SIZE size of displayed alignment text</li>
74 * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
75 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
76 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
77 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
78 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
79 * <li>SHOW_IDENTITY show percentage identity annotation</li>
80 * <li>SHOW_QUALITY show alignment quality annotation</li>
81 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
82 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
83 * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
84 * LABEL_AND_SEQUENCE</li>
85 * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
86 * sequence annotations</li>
87 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
89 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
90 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
91 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
92 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
93 * <li>VERSION the version of the jalview build</li>
94 * <li>BUILD_DATE date of this build</li>
95 * <li>LATEST_VERSION the latest jalview version advertised on the
96 * www.jalview.org</li>
97 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
99 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
100 * suffix to file</li>
101 * <li>RECENT_URL list of recently retrieved URLs</li>
102 * <li>RECENT_FILE list of recently opened files</li>
103 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
104 * <li>PROXY_SERVER the proxy</li>
105 * <li>PROXY_PORT</li>
106 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
108 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
110 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
111 * collecting usage statistics</li>
112 * <li>DAS_LOCAL_SOURCE list of local das sources</li>
113 * <li>SHOW_OVERVIEW boolean for overview window display</li>
114 * <li>ANTI_ALIAS boolean for smooth fonts</li>
115 * <li>RIGHT_ALIGN_IDS boolean</li>
116 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
117 * <li>PAD_GAPS boolean</li>
118 * <li>ID_ITALICS boolean</li>
119 * <li>SHOW_JV_SUFFIX</li>
120 * <li>WRAP_ALIGNMENT</li>
121 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
123 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
124 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
126 * <li>STORED_LINKS list of name|url pairs which user has entered but are not
128 * <li>DEFAULT_LINK name of single url to be used when user double clicks a
129 * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
130 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
131 * jalview.utils.GroupURLLink for more info</li>
132 * <li>DAS_REGISTRY_URL the registry to query</li>
133 * <li>DEFAULT_BROWSER for unix</li>
134 * <li>DAS_ACTIVE_SOURCE list of active sources</li>
135 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
137 * <li>VERSION_CHECK (true) check for the latest release version from
138 * www.jalview.org (or the alias given by the www.jalview.org property)</li>
139 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
141 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
143 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
144 * displayed as '.'</li>
145 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
146 * order of a newly displayed tree</li>
147 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
148 * sequence ID strings before attempting retrieval from any datasource</li>
149 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
151 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
152 * in the alignment.</li>
153 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
155 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
157 * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
158 * logo normalised to row height rather than histogram height.</li>
159 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
160 * respond to selections made in other alignments containing the same sequences.
162 * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
163 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
164 * warning dialog box is displayed.</li>
165 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
166 * when shading by annotation</li>
167 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
168 * when shading by annotation</li>
169 * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
170 * requests to be redirected to a mirror of http://www.jalview.org</li>
171 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
172 * alignment figure to accommodate even the longest sequence ID or annotation
174 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
175 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
176 * will override this).</li>
177 * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
179 * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
180 * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
182 * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
184 * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
186 * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
189 * Deprecated settings:
192 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
193 * startup (JWS1 services only)</li>
194 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
195 * (JWS1 services only)</li>
196 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
197 * services in the desktop GUI</li>
198 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
199 * panel in web service preferences</li>
203 * @version $Revision$
208 * property giving log4j level for CASTOR loggers
210 public static final String CASTORLOGLEVEL = "logs.Castor.level";
213 * property giving log4j level for AXIS loggers
215 public static final String AXISLOGLEVEL = "logs.Axis.level";
218 * property giving log4j level for Jalview Log
220 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
222 public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
224 public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
226 public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
231 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
232 .getProperty("user.home")
234 + ".sifts_downloads" + File.separatorChar;
236 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
238 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
241 * Identifiers.org download settings
243 private static final String ID_ORG_FILE = System.getProperty("user.home")
244 + File.separatorChar + ".jalview_identifiers";
246 private static final String ID_ORG_URL = "http://identifiers.org/rest/collections/";
249 * Allowed values are PDB or mmCIF
251 private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
254 private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
258 * a date formatter using a fixed (rather than the user's) locale;
259 * this ensures that date properties can be written and re-read successfully
260 * even if the user changes their locale setting
262 private static final DateFormat date_format = SimpleDateFormat
263 .getDateTimeInstance(SimpleDateFormat.MEDIUM,
264 SimpleDateFormat.MEDIUM, Locale.UK);
267 * Initialises the Jalview Application Log
269 public static Logger log;
271 /** Jalview Properties */
272 public static Properties applicationProperties = new Properties()
274 // override results in properties output in alphabetical order
276 public synchronized Enumeration<Object> keys()
278 return Collections.enumeration(new TreeSet<Object>(super.keySet()));
282 /** Default file is ~/.jalview_properties */
283 static String propertiesFile;
285 private static boolean propsAreReadOnly = false;
287 public static void initLogger()
295 // TODO: redirect stdout and stderr here in order to grab the output of
298 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
300 ap.setName("JalviewLogger");
301 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
303 Logger laxis = Logger.getLogger("org.apache.axis");
304 Logger lcastor = Logger.getLogger("org.exolab.castor");
305 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
307 laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
308 Level.INFO.toString())));
309 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
310 Level.INFO.toString())));
311 lcastor = Logger.getLogger("org.exolab.castor.xml");
312 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
313 Level.INFO.toString())));
314 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
315 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
316 // Level.INFO.toString())));
317 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
318 "logs.Jalview.level", Level.INFO.toString())));
319 // laxis.addAppender(ap);
320 // lcastor.addAppender(ap);
321 // jalview.bin.Cache.log.addAppender(ap);
322 // Tell the user that debug is enabled
323 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
324 } catch (Exception ex)
326 System.err.println("Problems initializing the log4j system\n");
327 ex.printStackTrace(System.err);
331 /** Called when Jalview is started */
332 public static void loadProperties(String propsFile)
334 propertiesFile = propsFile;
335 if (propsFile == null)
337 propertiesFile = System.getProperty("user.home") + File.separatorChar
338 + ".jalview_properties";
342 // don't corrupt the file we've been given.
343 propsAreReadOnly = true;
351 fis = new java.net.URL(propertiesFile).openStream();
352 System.out.println("Loading jalview properties from : "
355 .println("Disabling Jalview writing to user's local properties file.");
356 propsAreReadOnly = true;
358 } catch (Exception ex)
364 fis = new FileInputStream(propertiesFile);
366 applicationProperties.load(fis);
368 // remove any old build properties
370 deleteBuildProperties();
372 } catch (Exception ex)
374 System.out.println("Error reading properties file: " + ex);
377 if (getDefault("USE_PROXY", false))
379 String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
380 "PROXY_PORT", "8080");
382 System.out.println("Using proxyServer: " + proxyServer
383 + " proxyPort: " + proxyPort);
385 System.setProperty("http.proxyHost", proxyServer);
386 System.setProperty("http.proxyPort", proxyPort);
389 // LOAD THE AUTHORS FROM THE authors.props file
392 String authorDetails = "jar:".concat(Cache.class
393 .getProtectionDomain().getCodeSource().getLocation()
394 .toString().concat("!/authors.props"));
396 java.net.URL localJarFileURL = new java.net.URL(authorDetails);
398 InputStream in = localJarFileURL.openStream();
399 applicationProperties.load(in);
401 } catch (Exception ex)
403 System.out.println("Error reading author details: " + ex);
404 applicationProperties.remove("AUTHORS");
405 applicationProperties.remove("AUTHORFNAMES");
406 applicationProperties.remove("YEAR");
409 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
410 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
411 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
414 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
415 .getCodeSource().getLocation().toString()
416 .concat("!/.build_properties"));
418 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
420 InputStream in = localJarFileURL.openStream();
421 applicationProperties.load(in);
423 } catch (Exception ex)
425 System.out.println("Error reading build details: " + ex);
426 applicationProperties.remove("VERSION");
429 String jnlpVersion = System.getProperty("jalview.version");
430 String codeVersion = getProperty("VERSION");
431 String codeInstallation = getProperty("INSTALLATION");
432 if (codeVersion == null)
434 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
435 codeVersion = "Test";
436 jnlpVersion = "Test";
437 codeInstallation = "";
441 codeInstallation = " (" + codeInstallation + ")";
443 new BuildDetails(codeVersion, null, codeInstallation);
446 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
448 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
449 "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
451 SiftsSettings.setFailSafePIDThreshold(jalview.bin.Cache.getDefault(
452 "sifts_fail_safe_pid_threshold",
453 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
455 SiftsSettings.setCacheThresholdInDays(jalview.bin.Cache.getDefault(
456 "sifts_cache_threshold_in_days",
457 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
459 IdOrgSettings.setUrl(ID_ORG_URL);
460 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
463 .println("Jalview Version: " + codeVersion + codeInstallation);
465 StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
466 .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
467 StructureImportSettings
468 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
469 // StructureImportSettings
470 // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
471 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
472 // jnlpVersion will be null if we're using InstallAnywhere
473 // Dont do this check if running in headless mode
474 if (jnlpVersion == null
475 && getDefault("VERSION_CHECK", true)
476 && (System.getProperty("java.awt.headless") == null || System
477 .getProperty("java.awt.headless").equals("false")))
480 class VersionChecker extends Thread
485 String orgtimeout = System
486 .getProperty("sun.net.client.defaultConnectTimeout");
487 if (orgtimeout == null)
490 System.out.println("# INFO: Setting default net timeout to "
491 + orgtimeout + " seconds.");
493 String remoteVersion = null;
496 System.setProperty("sun.net.client.defaultConnectTimeout",
498 java.net.URL url = new java.net.URL(Cache.getDefault(
499 "www.jalview.org", "http://www.jalview.org")
500 + "/webstart/jalview.jnlp");
501 BufferedReader in = new BufferedReader(new InputStreamReader(
504 while ((line = in.readLine()) != null)
506 if (line.indexOf("jalview.version") == -1)
511 line = line.substring(line.indexOf("value=") + 7);
512 line = line.substring(0, line.lastIndexOf("\""));
513 remoteVersion = line;
516 } catch (Exception ex)
519 .println("Non-fatal exception when checking version at www.jalview.org :");
520 System.out.println(ex);
521 remoteVersion = getProperty("VERSION");
523 System.setProperty("sun.net.client.defaultConnectTimeout",
526 setProperty("LATEST_VERSION", remoteVersion);
530 VersionChecker vc = new VersionChecker();
535 if (jnlpVersion != null)
537 setProperty("LATEST_VERSION", jnlpVersion);
541 applicationProperties.remove("LATEST_VERSION");
545 setProperty("VERSION", codeVersion);
547 // LOAD USERDEFINED COLOURS
548 jalview.gui.UserDefinedColours
549 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
550 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
554 private static void deleteBuildProperties()
556 applicationProperties.remove("LATEST_VERSION");
557 applicationProperties.remove("VERSION");
558 applicationProperties.remove("AUTHORS");
559 applicationProperties.remove("AUTHORFNAMES");
560 applicationProperties.remove("YEAR");
561 applicationProperties.remove("BUILD_DATE");
562 applicationProperties.remove("INSTALLATION");
566 * Gets Jalview application property of given key. Returns null if key not
572 * @return Property value
574 public static String getProperty(String key)
576 return applicationProperties.getProperty(key);
580 * These methods are used when checking if the saved preference is different
581 * to the default setting
584 public static boolean getDefault(String property, boolean def)
586 String string = getProperty(property);
589 def = Boolean.valueOf(string).booleanValue();
596 * These methods are used when checking if the saved preference is different
597 * to the default setting
599 public static String getDefault(String property, String def)
601 String string = getProperty(property);
611 * Stores property in the file "HOME_DIR/.jalview_properties"
616 * String value of property
618 * @return String value of property
620 public static String setProperty(String key, String obj)
625 applicationProperties.setProperty(key, obj);
626 if (!propsAreReadOnly)
628 FileOutputStream out = new FileOutputStream(propertiesFile);
629 applicationProperties.store(out, "---JalviewX Properties File---");
632 } catch (Exception ex)
634 System.out.println("Error setting property: " + key + " " + obj
641 * remove the specified property from the jalview properties file
645 public static void removeProperty(String string)
647 applicationProperties.remove(string);
652 * save the properties to the jalview properties path
654 public static void saveProperties()
656 if (!propsAreReadOnly)
660 FileOutputStream out = new FileOutputStream(propertiesFile);
661 applicationProperties.store(out, "---JalviewX Properties File---");
663 } catch (Exception ex)
665 System.out.println("Error saving properties: " + ex);
671 * internal vamsas class discovery state
673 private static int vamsasJarsArePresent = -1;
676 * Searches for vamsas client classes on class path.
678 * @return true if vamsas client is present on classpath
680 public static boolean vamsasJarsPresent()
682 if (vamsasJarsArePresent == -1)
686 if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
687 "uk.ac.vamsas.client.VorbaId") != null)
689 jalview.bin.Cache.log
690 .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
691 vamsasJarsArePresent = 1;
692 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
693 lvclient.setLevel(Level.toLevel(Cache.getDefault(
694 "logs.Vamsas.Level", Level.INFO.toString())));
696 lvclient.addAppender(log.getAppender("JalviewLogger"));
697 // Tell the user that debug is enabled
698 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
700 } catch (Exception e)
702 vamsasJarsArePresent = 0;
703 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
706 return (vamsasJarsArePresent > 0);
710 * internal vamsas class discovery state
712 private static int groovyJarsArePresent = -1;
715 * Searches for vamsas client classes on class path.
717 * @return true if vamsas client is present on classpath
719 public static boolean groovyJarsPresent()
721 if (groovyJarsArePresent == -1)
725 if (Cache.class.getClassLoader().loadClass(
726 "groovy.lang.GroovyObject") != null)
728 jalview.bin.Cache.log
729 .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
730 groovyJarsArePresent = 1;
731 Logger lgclient = Logger.getLogger("groovy");
732 lgclient.setLevel(Level.toLevel(Cache.getDefault(
733 "logs.Groovy.Level", Level.INFO.toString())));
735 lgclient.addAppender(log.getAppender("JalviewLogger"));
736 // Tell the user that debug is enabled
737 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
741 groovyJarsArePresent = 0;
742 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
743 } catch (Exception e)
745 groovyJarsArePresent = 0;
746 jalview.bin.Cache.log.debug("Groovy Classes are not present");
749 return (groovyJarsArePresent > 0);
753 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
756 protected static Object tracker = null;
758 protected static Class trackerfocus = null;
760 protected static Class jgoogleanalyticstracker = null;
763 * Initialise the google tracker if it is not done already.
765 public static void initGoogleTracker()
769 if (jgoogleanalyticstracker == null)
771 // try to get the tracker class
774 jgoogleanalyticstracker = Cache.class
777 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
778 trackerfocus = Cache.class.getClassLoader().loadClass(
779 "com.boxysystems.jgoogleanalytics.FocusPoint");
780 } catch (Exception e)
782 log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
784 jgoogleanalyticstracker = null;
789 // now initialise tracker
790 Exception re = null, ex = null;
792 String vrs = "No Version Accessible";
795 // Google analytics tracking code for Library Finder
796 tracker = jgoogleanalyticstracker.getConstructor(
797 new Class[] { String.class, String.class, String.class })
801 (vrs = jalview.bin.Cache.getProperty("VERSION")
803 + jalview.bin.Cache.getDefault(
804 "BUILD_DATE", "unknown")),
806 jgoogleanalyticstracker.getMethod("trackAsynchronously",
807 new Class[] { trackerfocus }).invoke(
809 new Object[] { trackerfocus.getConstructor(
810 new Class[] { String.class }).newInstance(
811 new Object[] { "Application Started." }) });
812 } catch (RuntimeException e)
815 } catch (Exception e)
822 if (re != null || ex != null || err != null)
828 log.debug("Caught runtime exception in googletracker init:", re);
833 "Failed to initialise GoogleTracker for Jalview Desktop with version "
839 "Whilst initing GoogleTracker for Jalview Desktop version "
848 .println("Debug: Caught runtime exception in googletracker init:"
850 re.printStackTrace();
855 .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
857 ex.printStackTrace();
863 .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
865 err.printStackTrace();
871 log.debug("Successfully initialised tracker.");
877 * get the user's default colour if available
883 public static Color getDefaultColour(String property, Color defcolour)
885 String colprop = getProperty(property);
890 Color col = jalview.schemes.ColourSchemeProperty
891 .getAWTColorFromName(colprop);
896 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
897 } catch (Exception ex)
899 log.warn("Couldn't parse '" + colprop + "' as a colour for "
904 return (col == null) ? defcolour : col;
908 * store a colour as a Jalview user default property
913 public static void setColourProperty(String property, Color colour)
915 setProperty(property, jalview.util.Format.getHexString(colour));
919 * Stores a formatted date in a jalview property, using a fixed locale.
921 * @param propertyName
923 * @return the formatted date string
925 public static String setDateProperty(String propertyName, Date date)
927 String formatted = date_format.format(date);
928 setProperty(propertyName, formatted);
933 * Reads a date stored in a Jalview property, parses it (using a fixed locale
934 * format) and returns as a Date, or null if parsing fails
936 * @param propertyName
940 public static Date getDateProperty(String propertyName)
942 String val = getProperty(propertyName);
947 return date_format.parse(val);
948 } catch (Exception ex)
950 System.err.println("Invalid or corrupt date in property '"
951 + propertyName + "' : value was '" + val + "'");
958 * get and parse a property as an integer. send any parsing problems to
962 * @return null or Integer
964 public static Integer getIntegerProperty(String property)
966 String val = getProperty(property);
967 if (val != null && (val = val.trim()).length() > 0)
971 return Integer.valueOf(val);
972 } catch (NumberFormatException x)
974 System.err.println("Invalid integer in property '" + property
975 + "' (value was '" + val + "')");
981 private static DasSourceRegistryI sourceRegistry = null;
986 * @return instance of the das source registry
988 public static DasSourceRegistryI getDasSourceRegistry()
990 if (sourceRegistry == null)
992 sourceRegistry = new DasSourceRegistry();
994 return sourceRegistry;
998 * Set the specified value, or remove it if null or empty. Does not save the
1004 public static void setOrRemove(String propName, String value)
1006 if (propName == null)
1010 if (value == null || value.trim().length() < 1)
1012 Cache.applicationProperties.remove(propName);
1016 Cache.applicationProperties.setProperty(propName, value);