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.gui.UserDefinedColours;
25 import jalview.schemes.ColourSchemeLoader;
26 import jalview.schemes.ColourSchemes;
27 import jalview.schemes.UserColourScheme;
28 import jalview.structure.StructureImportSettings;
29 import jalview.urls.IdOrgSettings;
30 import jalview.util.ColorUtils;
31 import jalview.util.Platform;
32 import jalview.ws.sifts.SiftsSettings;
34 import java.awt.Color;
35 import java.io.BufferedReader;
37 import java.io.FileInputStream;
38 import java.io.FileOutputStream;
39 import java.io.InputStream;
40 import java.io.InputStreamReader;
42 import java.text.DateFormat;
43 import java.text.SimpleDateFormat;
44 import java.util.Collections;
45 import java.util.Date;
46 import java.util.Enumeration;
47 import java.util.Locale;
48 import java.util.Properties;
49 import java.util.StringTokenizer;
50 import java.util.TreeSet;
52 import org.apache.log4j.ConsoleAppender;
53 import org.apache.log4j.Level;
54 import org.apache.log4j.Logger;
55 import org.apache.log4j.SimpleLayout;
58 * Stores and retrieves Jalview Application Properties Lists and fields within
59 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
60 * are alternative values for a tag. <br>
62 * Current properties include:
65 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
66 * logging level for axis (used for web services) <br>
68 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
69 * the logging level for castor (used for serialization) <br>
71 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
73 * <li>SCREEN_WIDTH</li>
74 * <li>SCREEN_HEIGHT</li>
75 * <li>SCREEN_Y=285</li>
76 * <li>SCREEN_X=371</li>
77 * <li>SHOW_FULLSCREEN boolean</li>
78 * <li>FONT_NAME java font name for alignment text display</li>
79 * <li>FONT_SIZE size of displayed alignment text</li>
80 * <li>FONT_STYLE style of font displayed (sequence labels are always
82 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
83 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
84 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
85 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
86 * <li>SHOW_IDENTITY show percentage identity annotation</li>
87 * <li>SHOW_QUALITY show alignment quality annotation</li>
88 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
89 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
90 * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
91 * LABEL_AND_SEQUENCE</li>
92 * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
93 * sequence annotations</li>
94 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
96 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
97 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
98 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
99 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
100 * <li>VERSION the version of the jalview build</li>
101 * <li>BUILD_DATE date of this build</li>
102 * <li>LATEST_VERSION the latest jalview version advertised on the
103 * www.jalview.org</li>
104 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
106 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
107 * suffix to file</li>
108 * <li>RECENT_URL list of recently retrieved URLs</li>
109 * <li>RECENT_FILE list of recently opened files</li>
110 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
111 * <li>PROXY_SERVER the proxy</li>
112 * <li>PROXY_PORT</li>
113 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
115 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
117 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
118 * collecting usage statistics</li>
119 * <li>SHOW_OVERVIEW boolean for overview window display</li>
120 * <li>ANTI_ALIAS boolean for smooth fonts</li>
121 * <li>RIGHT_ALIGN_IDS boolean</li>
122 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
123 * <li>PAD_GAPS boolean</li>
124 * <li>ID_ITALICS boolean</li>
125 * <li>SHOW_JV_SUFFIX</li>
126 * <li>WRAP_ALIGNMENT</li>
127 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
129 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
130 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
132 * <li>STORED_LINKS list of name|url pairs which user has entered but are not
134 * <li>DEFAULT_LINK name of single url to be used when user double clicks a
135 * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
136 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
137 * jalview.utils.GroupURLLink for more info</li>
138 * <li>DEFAULT_BROWSER for unix</li>
139 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
141 * <li>VERSION_CHECK (true) check for the latest release version from
142 * www.jalview.org (or the alias given by the www.jalview.org property)</li>
143 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
145 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
147 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
148 * displayed as '.'</li>
149 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
150 * order of a newly displayed tree</li>
151 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
152 * sequence ID strings before attempting retrieval from any datasource</li>
153 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
155 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
156 * in the alignment.</li>
157 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
159 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
161 * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
162 * logo normalised to row height rather than histogram height.</li>
163 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
164 * respond to selections made in other alignments containing the same sequences.
166 * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
167 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
168 * warning dialog box is displayed.</li>
169 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
170 * when shading by annotation</li>
171 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
172 * when shading by annotation</li>
173 * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
174 * requests to be redirected to a mirror of http://www.jalview.org</li>
175 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
176 * alignment figure to accommodate even the longest sequence ID or annotation
178 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
179 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
180 * will override this).</li>
181 * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
183 * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
184 * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
186 * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
188 * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
190 * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
191 * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
195 * Deprecated settings:
198 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
199 * startup (JWS1 services only)</li>
200 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
201 * (JWS1 services only)</li>
202 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
203 * services in the desktop GUI</li>
204 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
205 * panel in web service preferences</li>
209 * @version $Revision$
214 * property giving log4j level for CASTOR loggers
216 public static final String CASTORLOGLEVEL = "logs.Castor.level";
219 * property giving log4j level for AXIS loggers
221 public static final String AXISLOGLEVEL = "logs.Axis.level";
224 * property giving log4j level for Jalview Log
226 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
231 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
232 .getProperty("user.home") + File.separatorChar
233 + ".sifts_downloads" + File.separatorChar;
235 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
237 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
240 * Identifiers.org download settings
242 private static final String ID_ORG_FILE = System.getProperty("user.home")
243 + File.separatorChar + ".identifiers.org.ids.json";
246 * Allowed values are PDB or mmCIF
248 private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
251 private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
255 * a date formatter using a fixed (rather than the user's) locale;
256 * this ensures that date properties can be written and re-read successfully
257 * even if the user changes their locale setting
259 private static final DateFormat date_format = SimpleDateFormat
260 .getDateTimeInstance(SimpleDateFormat.MEDIUM,
261 SimpleDateFormat.MEDIUM, Locale.UK);
264 * Initialises the Jalview Application Log
266 public static Logger log;
268 /** Jalview Properties */
269 public static Properties applicationProperties = new Properties()
271 // override results in properties output in alphabetical order
273 public synchronized Enumeration<Object> keys()
275 return Collections.enumeration(new TreeSet<>(super.keySet()));
279 /** Default file is ~/.jalview_properties */
280 static String propertiesFile;
282 private static boolean propsAreReadOnly = Platform.isJS();
284 private final static String JS_PROPERTY_PREFIX = "jalview_";
286 public static void initLogger()
294 // TODO: redirect stdout and stderr here in order to grab the output of
297 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
299 ap.setName("JalviewLogger");
300 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
302 Logger laxis = Logger.getLogger("org.apache.axis");
303 Logger lcastor = Logger.getLogger("org.exolab.castor");
304 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
306 laxis.setLevel(Level.toLevel(
307 Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
308 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
309 Level.INFO.toString())));
310 lcastor = Logger.getLogger("org.exolab.castor.xml");
311 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
312 Level.INFO.toString())));
313 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
314 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
315 // Level.INFO.toString())));
316 // we shouldn't need to do this
317 org.apache.log4j.Logger.getRootLogger().setLevel(org.apache.log4j.Level.INFO);
319 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
320 .getDefault("logs.Jalview.level", Level.INFO.toString())));
321 // laxis.addAppender(ap);
322 // lcastor.addAppender(ap);
323 // jalview.bin.Cache.log.addAppender(ap);
324 // Tell the user that debug is enabled
325 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
326 } catch (Exception ex)
328 System.err.println("Problems initializing the log4j system\n");
329 ex.printStackTrace(System.err);
334 * Loads properties from the given properties file. Any existing properties
337 public static void loadProperties(String propsFile)
339 propertiesFile = propsFile;
340 if (propsFile == null && !propsAreReadOnly)
342 propertiesFile = System.getProperty("user.home") + File.separatorChar
343 + ".jalview_properties";
347 // don't corrupt the file we've been given.
348 propsAreReadOnly = true;
351 if (propertiesFile == null)
353 Platform.readInfoProperties(JS_PROPERTY_PREFIX,
354 applicationProperties);
363 fis = new java.net.URL(propertiesFile).openStream();
365 "Loading jalview properties from : " + propertiesFile);
367 "Disabling Jalview writing to user's local properties file.");
368 propsAreReadOnly = true;
370 } catch (Exception ex)
376 fis = new FileInputStream(propertiesFile);
378 applicationProperties.clear();
379 applicationProperties.load(fis);
381 // remove any old build properties
383 deleteBuildProperties();
385 } catch (Exception ex)
387 System.out.println("Error reading properties file: " + ex);
390 if (getDefault("USE_PROXY", false))
392 String proxyServer = getDefault("PROXY_SERVER", ""),
393 proxyPort = getDefault("PROXY_PORT", "8080");
395 System.out.println("Using proxyServer: " + proxyServer
396 + " proxyPort: " + proxyPort);
398 System.setProperty("http.proxyHost", proxyServer);
399 System.setProperty("http.proxyPort", proxyPort);
402 // LOAD THE AUTHORS FROM THE authors.props file
403 String authorDetails = resolveResourceURLFor("/authors.props");
407 if (authorDetails != null)
409 URL localJarFileURL = new URL(authorDetails);
410 InputStream in = localJarFileURL.openStream();
411 applicationProperties.load(in);
414 } catch (Exception ex)
416 System.out.println("Error reading author details: " + ex);
417 authorDetails = null;
419 if (authorDetails == null)
421 applicationProperties.remove("AUTHORS");
422 applicationProperties.remove("AUTHORFNAMES");
423 applicationProperties.remove("YEAR");
426 loadBuildProperties(false);
429 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
431 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
432 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
434 SiftsSettings.setFailSafePIDThreshold(
435 jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
436 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
438 SiftsSettings.setCacheThresholdInDays(
439 jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
440 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
442 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
443 "http://www.jalview.org/services/identifiers"));
444 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
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));
454 String jnlpVersion = System.getProperty("jalview.version");
456 // jnlpVersion will be null if a latest version check for the channel needs to
458 // Dont do this check if running in headless mode
460 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
461 && (System.getProperty("java.awt.headless") == null || System
462 .getProperty("java.awt.headless").equals("false")))
469 String orgtimeout = System
470 .getProperty("sun.net.client.defaultConnectTimeout");
471 if (orgtimeout == null)
474 System.out.println("# INFO: Setting default net timeout to "
475 + orgtimeout + " seconds.");
477 String remoteVersion = null;
480 System.setProperty("sun.net.client.defaultConnectTimeout",
482 java.net.URL url = new java.net.URL(Cache
483 .getDefault("www.jalview.org", "http://www.jalview.org")
484 + "/webstart/jalview.jnlp");
485 BufferedReader in = new BufferedReader(
486 new InputStreamReader(url.openStream()));
488 while ((line = in.readLine()) != null)
490 if (line.indexOf("jalview.version") == -1)
495 line = line.substring(line.indexOf("value=") + 7);
496 line = line.substring(0, line.lastIndexOf("\""));
497 remoteVersion = line;
500 } catch (Exception ex)
503 "Non-fatal exception when checking version at www.jalview.org :");
504 System.out.println(ex);
505 remoteVersion = getProperty("VERSION");
507 System.setProperty("sun.net.client.defaultConnectTimeout",
510 setProperty("LATEST_VERSION", remoteVersion);
516 if (jnlpVersion != null)
518 setProperty("LATEST_VERSION", jnlpVersion);
522 applicationProperties.remove("LATEST_VERSION");
526 // LOAD USERDEFINED COLOURS
527 Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
528 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
533 * construct a resource URL for the given absolute resource pathname
535 * @param resourcePath
538 private static String resolveResourceURLFor(String resourcePath)
541 if (Platform.isJS() || !Cache.class.getProtectionDomain()
542 .getCodeSource().getLocation().toString().endsWith(".jar"))
546 url = Cache.class.getResource(resourcePath).toString();
547 } catch (Exception ex)
549 System.err.println("Failed to resolve resource " + resourcePath + ": "
555 url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
556 .getLocation().toString().concat("!" + resourcePath));
561 public static void loadBuildProperties(boolean reportVersion)
563 String codeInstallation = getProperty("INSTALLATION");
564 boolean printVersion = codeInstallation == null;
567 * read build properties - from the Jalview jar for a Java distribution,
568 * or from codebase file in test or JalviewJS context
572 String buildDetails = resolveResourceURLFor("/.build_properties");
573 URL localJarFileURL = new URL(buildDetails);
574 InputStream in = localJarFileURL.openStream();
575 applicationProperties.load(in);
577 } catch (Exception ex)
579 System.out.println("Error reading build details: " + ex);
580 applicationProperties.remove("VERSION");
582 String codeVersion = getProperty("VERSION");
583 codeInstallation = getProperty("INSTALLATION");
585 if (codeVersion == null)
587 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
588 codeVersion = "Test";
589 codeInstallation = "";
593 codeInstallation = " (" + codeInstallation + ")";
595 setProperty("VERSION", codeVersion);
596 new BuildDetails(codeVersion, null, codeInstallation);
597 if (printVersion && reportVersion)
600 .println("Jalview Version: " + codeVersion + codeInstallation);
604 private static void deleteBuildProperties()
606 applicationProperties.remove("LATEST_VERSION");
607 applicationProperties.remove("VERSION");
608 applicationProperties.remove("AUTHORS");
609 applicationProperties.remove("AUTHORFNAMES");
610 applicationProperties.remove("YEAR");
611 applicationProperties.remove("BUILD_DATE");
612 applicationProperties.remove("INSTALLATION");
616 * Gets Jalview application property of given key. Returns null if key not
622 * @return Property value
624 public static String getProperty(String key)
626 String prop = applicationProperties.getProperty(key);
627 if (prop == null && Platform.isJS())
629 prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
630 + "_" + JS_PROPERTY_PREFIX + key);
636 * These methods are used when checking if the saved preference is different
637 * to the default setting
640 public static boolean getDefault(String property, boolean def)
642 String string = getProperty(property);
645 def = Boolean.valueOf(string).booleanValue();
651 public static int getDefault(String property, int def)
653 String string = getProperty(property);
658 def = Integer.parseInt(string);
659 } catch (NumberFormatException e)
661 System.out.println("Error parsing int property '" + property
662 + "' with value '" + string + "'");
670 * Answers the value of the given property, or the supplied default value if
671 * the property is not set
673 public static String getDefault(String property, String def)
675 String value = getProperty(property);
676 return value == null ? def : value;
680 * Stores property in the file "HOME_DIR/.jalview_properties"
685 * String value of property
687 * @return previous value of property (or null)
689 public static Object setProperty(String key, String obj)
691 Object oldValue = null;
694 oldValue = applicationProperties.setProperty(key, obj);
695 if (propertiesFile != null && !propsAreReadOnly)
697 FileOutputStream out = new FileOutputStream(propertiesFile);
698 applicationProperties.store(out, "---JalviewX Properties File---");
701 } catch (Exception ex)
704 "Error setting property: " + key + " " + obj + "\n" + ex);
710 * remove the specified property from the jalview properties file
714 public static void removeProperty(String string)
716 applicationProperties.remove(string);
721 * save the properties to the jalview properties path
723 public static void saveProperties()
725 if (!propsAreReadOnly)
729 FileOutputStream out = new FileOutputStream(propertiesFile);
730 applicationProperties.store(out, "---JalviewX Properties File---");
732 } catch (Exception ex)
734 System.out.println("Error saving properties: " + ex);
740 * internal vamsas class discovery state
742 private static int vamsasJarsArePresent = -1;
745 * Searches for vamsas client classes on class path.
747 * @return true if vamsas client is present on classpath
749 public static boolean vamsasJarsPresent()
751 if (vamsasJarsArePresent == -1)
755 if (jalview.jbgui.GDesktop.class.getClassLoader()
756 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
758 jalview.bin.Cache.log.debug(
759 "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
760 vamsasJarsArePresent = 1;
761 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
762 lvclient.setLevel(Level.toLevel(Cache
763 .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
765 lvclient.addAppender(log.getAppender("JalviewLogger"));
766 // Tell the user that debug is enabled
767 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
769 } catch (Exception e)
771 vamsasJarsArePresent = 0;
772 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
775 return (vamsasJarsArePresent > 0);
779 * internal vamsas class discovery state
781 private static int groovyJarsArePresent = -1;
784 * Searches for vamsas client classes on class path.
786 * @return true if vamsas client is present on classpath
788 public static boolean groovyJarsPresent()
790 if (groovyJarsArePresent == -1)
794 if (Cache.class.getClassLoader()
795 .loadClass("groovy.lang.GroovyObject") != null)
797 jalview.bin.Cache.log.debug(
798 "Found Groovy (groovy.lang.GroovyObject can be loaded)");
799 groovyJarsArePresent = 1;
800 Logger lgclient = Logger.getLogger("groovy");
801 lgclient.setLevel(Level.toLevel(Cache
802 .getDefault("logs.Groovy.Level", Level.INFO.toString())));
804 lgclient.addAppender(log.getAppender("JalviewLogger"));
805 // Tell the user that debug is enabled
806 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
810 groovyJarsArePresent = 0;
811 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
812 } catch (Exception e)
814 groovyJarsArePresent = 0;
815 jalview.bin.Cache.log.debug("Groovy Classes are not present");
818 return (groovyJarsArePresent > 0);
822 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
825 protected static Object tracker = null;
827 protected static Class trackerfocus = null;
829 protected static Class jgoogleanalyticstracker = null;
832 * Initialise the google tracker if it is not done already.
834 public static void initGoogleTracker()
838 if (jgoogleanalyticstracker == null)
840 // try to get the tracker class
843 jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
844 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
845 trackerfocus = Cache.class.getClassLoader()
846 .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
847 } catch (Exception e)
850 "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
852 jgoogleanalyticstracker = null;
857 // now initialise tracker
858 Exception re = null, ex = null;
860 String vrs = "No Version Accessible";
863 // Google analytics tracking code for Library Finder
864 tracker = jgoogleanalyticstracker
865 .getConstructor(new Class[]
866 { String.class, String.class, String.class })
867 .newInstance(new Object[]
869 (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
870 + jalview.bin.Cache.getDefault("BUILD_DATE",
873 jgoogleanalyticstracker
874 .getMethod("trackAsynchronously", new Class[]
876 .invoke(tracker, new Object[]
877 { trackerfocus.getConstructor(new Class[] { String.class })
878 .newInstance(new Object[]
879 { "Application Started." }) });
880 } catch (RuntimeException e)
883 } catch (Exception e)
890 if (re != null || ex != null || err != null)
896 log.debug("Caught runtime exception in googletracker init:",
902 "Failed to initialise GoogleTracker for Jalview Desktop with version "
909 "Whilst initing GoogleTracker for Jalview Desktop version "
919 "Debug: Caught runtime exception in googletracker init:"
921 re.printStackTrace();
926 "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
928 ex.printStackTrace();
934 "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
936 err.printStackTrace();
942 log.debug("Successfully initialised tracker.");
948 * get the user's default colour if available
954 public static Color getDefaultColour(String property, Color defcolour)
956 String colprop = getProperty(property);
961 Color col = ColorUtils.parseColourString(colprop);
964 log.warn("Couldn't parse '" + colprop + "' as a colour for "
967 return (col == null) ? defcolour : col;
971 * store a colour as a Jalview user default property
976 public static void setColourProperty(String property, Color colour)
978 setProperty(property, jalview.util.Format.getHexString(colour));
982 * Stores a formatted date in a jalview property, using a fixed locale.
984 * @param propertyName
986 * @return the formatted date string
988 public static String setDateProperty(String propertyName, Date date)
990 String formatted = date_format.format(date);
991 setProperty(propertyName, formatted);
996 * Reads a date stored in a Jalview property, parses it (using a fixed locale
997 * format) and returns as a Date, or null if parsing fails
999 * @param propertyName
1003 public static Date getDateProperty(String propertyName)
1005 String val = getProperty(propertyName);
1010 return date_format.parse(val);
1011 } catch (Exception ex)
1013 System.err.println("Invalid or corrupt date in property '"
1014 + propertyName + "' : value was '" + val + "'");
1021 * get and parse a property as an integer. send any parsing problems to
1025 * @return null or Integer
1027 public static Integer getIntegerProperty(String property)
1029 String val = getProperty(property);
1030 if (val != null && (val = val.trim()).length() > 0)
1034 return Integer.valueOf(val);
1035 } catch (NumberFormatException x)
1037 System.err.println("Invalid integer in property '" + property
1038 + "' (value was '" + val + "')");
1045 * Set the specified value, or remove it if null or empty. Does not save the
1051 public static void setOrRemove(String propName, String value)
1053 if (propName == null)
1057 if (value == null || value.trim().length() < 1)
1059 Cache.applicationProperties.remove(propName);
1063 Cache.applicationProperties.setProperty(propName, value);
1068 * Loads in user colour schemes from files.
1071 * a '|'-delimited list of file paths
1073 public static void initUserColourSchemes(String files)
1075 if (files == null || files.length() == 0)
1080 // In case colours can't be loaded, we'll remove them
1081 // from the default list here.
1082 StringBuffer coloursFound = new StringBuffer();
1083 StringTokenizer st = new StringTokenizer(files, "|");
1084 while (st.hasMoreElements())
1086 String file = st.nextToken();
1089 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1092 if (coloursFound.length() > 0)
1094 coloursFound.append("|");
1096 coloursFound.append(file);
1097 ColourSchemes.getInstance().registerColourScheme(ucs);
1099 } catch (Exception ex)
1101 System.out.println("Error loading User ColourFile\n" + ex);
1104 if (!files.equals(coloursFound.toString()))
1106 if (coloursFound.toString().length() > 1)
1108 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1109 coloursFound.toString());
1113 applicationProperties
1114 .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1120 * Initial logging information helper for various versions output
1124 * @param defaultValue
1126 private static void appendIfNotNull(StringBuilder sb, String prefix,
1127 String value, String suffix, String defaultValue)
1129 if (value == null && defaultValue == null)
1133 String line = prefix + (value != null ? value : defaultValue) + suffix;
1139 * @return Jalview version, build details and JVM platform version for console
1141 public static String getVersionDetailsForConsole()
1143 StringBuilder sb = new StringBuilder();
1144 sb.append("Jalview Version: " + jalview.bin.Cache.getDefault("VERSION", "TEST"));
1146 sb.append("Jalview Installation: "
1147 + jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
1149 sb.append("Build Date: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
1151 sb.append("Java version: " + System.getProperty("java.version"));
1153 sb.append(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version"));
1155 appendIfNotNull(sb, "Install4j version: ",
1156 System.getProperty("sys.install4jVersion"), "\n", null);
1157 appendIfNotNull(sb, "Install4j template version: ",
1158 System.getProperty("installer_template_version"), "\n", null);
1159 appendIfNotNull(sb, "Launcher version: ",
1160 System.getProperty("launcher_version"), "\n", null);
1161 if (jalview.bin.Cache.getDefault("VERSION", "TEST").equals("DEVELOPMENT")) {
1162 appendIfNotNull(sb, "Getdown appdir: ",
1163 System.getProperty("getdownappdir"), "\n", null);
1164 appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
1167 return sb.toString();
1172 * @return build details as reported in splashscreen
1174 public static String getBuildDetailsForSplash()
1176 // consider returning more human friendly info
1177 // eg 'built from Source' or update channel
1178 return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");