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 java.awt.Color;
24 import java.io.BufferedReader;
26 import java.io.FileInputStream;
27 import java.io.FileOutputStream;
28 import java.io.InputStream;
29 import java.io.InputStreamReader;
30 import java.io.PrintWriter;
31 import java.io.StringWriter;
32 import java.text.DateFormat;
33 import java.text.SimpleDateFormat;
34 import java.util.Collections;
35 import java.util.Date;
36 import java.util.Enumeration;
37 import java.util.Locale;
38 import java.util.Properties;
39 import java.util.StringTokenizer;
40 import java.util.TreeSet;
41 import java.util.regex.Pattern;
43 import javax.swing.LookAndFeel;
44 import javax.swing.UIManager;
46 import org.apache.log4j.ConsoleAppender;
47 import org.apache.log4j.Level;
48 import org.apache.log4j.Logger;
49 import org.apache.log4j.SimpleLayout;
51 import jalview.datamodel.PDBEntry;
52 import jalview.gui.UserDefinedColours;
53 import jalview.schemes.ColourSchemeLoader;
54 import jalview.schemes.ColourSchemes;
55 import jalview.schemes.UserColourScheme;
56 import jalview.structure.StructureImportSettings;
57 import jalview.urls.IdOrgSettings;
58 import jalview.util.ColorUtils;
59 import jalview.ws.sifts.SiftsSettings;
62 * Stores and retrieves Jalview Application Properties Lists and fields within
63 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
64 * are alternative values for a tag. <br>
66 * Current properties include:
69 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
70 * logging level for axis (used for web services) <br>
72 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
73 * the logging level for castor (used for serialization) <br>
75 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
77 * <li>SCREEN_WIDTH</li>
78 * <li>SCREEN_HEIGHT</li>
79 * <li>SCREEN_Y=285</li>
80 * <li>SCREEN_X=371</li>
81 * <li>SHOW_FULLSCREEN boolean</li>
82 * <li>FONT_NAME java font name for alignment text display</li>
83 * <li>FONT_SIZE size of displayed alignment text</li>
84 * <li>FONT_STYLE style of font displayed (sequence labels are always
86 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
87 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
88 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
89 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
90 * <li>SHOW_IDENTITY show percentage identity annotation</li>
91 * <li>SHOW_QUALITY show alignment quality annotation</li>
92 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
93 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
94 * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
95 * LABEL_AND_SEQUENCE</li>
96 * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
97 * sequence annotations</li>
98 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
100 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
101 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
102 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
103 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
104 * <li>VERSION the version of the jalview build</li>
105 * <li>BUILD_DATE date of this build</li>
106 * <li>LATEST_VERSION the latest jalview version advertised on the
107 * www.jalview.org</li>
108 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
110 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
111 * suffix to file</li>
112 * <li>RECENT_URL list of recently retrieved URLs</li>
113 * <li>RECENT_FILE list of recently opened files</li>
114 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
115 * <li>PROXY_SERVER the proxy</li>
116 * <li>PROXY_PORT</li>
117 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
119 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
121 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
122 * collecting usage statistics</li>
123 * <li>SHOW_OVERVIEW boolean for overview window display</li>
124 * <li>ANTI_ALIAS boolean for smooth fonts</li>
125 * <li>RIGHT_ALIGN_IDS boolean</li>
126 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
127 * <li>PAD_GAPS boolean</li>
128 * <li>ID_ITALICS boolean</li>
129 * <li>SHOW_JV_SUFFIX</li>
130 * <li>WRAP_ALIGNMENT</li>
131 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
133 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
134 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
136 * <li>STORED_LINKS list of name|url pairs which user has entered but are not
138 * <li>DEFAULT_LINK name of single url to be used when user double clicks a
139 * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
140 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
141 * jalview.utils.GroupURLLink for more info</li>
142 * <li>DEFAULT_BROWSER for unix</li>
143 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
145 * <li>VERSION_CHECK (true) check for the latest release version from
146 * www.jalview.org (or the alias given by the www.jalview.org property)</li>
147 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
149 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
151 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
152 * displayed as '.'</li>
153 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
154 * order of a newly displayed tree</li>
155 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
156 * sequence ID strings before attempting retrieval from any datasource</li>
157 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
159 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
160 * in the alignment.</li>
161 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
163 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
165 * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
166 * logo normalised to row height rather than histogram height.</li>
167 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
168 * respond to selections made in other alignments containing the same sequences.
170 * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
171 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
172 * warning dialog box is displayed.</li>
173 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
174 * when shading by annotation</li>
175 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
176 * when shading by annotation</li>
177 * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
178 * requests to be redirected to a mirror of https://www.jalview.org</li>
179 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
180 * alignment figure to accommodate even the longest sequence ID or annotation
182 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
183 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
184 * will override this).</li>
185 * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
187 * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
188 * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
190 * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
192 * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
194 * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
195 * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
199 * Deprecated settings:
202 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
203 * startup (JWS1 services only)</li>
204 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
205 * (JWS1 services only)</li>
206 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
207 * services in the desktop GUI</li>
208 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
209 * panel in web service preferences</li>
213 * @version $Revision$
218 * property giving log4j level for CASTOR loggers
220 public static final String CASTORLOGLEVEL = "logs.Castor.level";
223 * property giving log4j level for AXIS loggers
225 public static final String AXISLOGLEVEL = "logs.Axis.level";
228 * property giving log4j level for Jalview Log
230 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
235 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
236 .getProperty("user.home") + File.separatorChar
237 + ".sifts_downloads" + File.separatorChar;
239 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
241 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
244 * Identifiers.org download settings
246 private static final String ID_ORG_FILE = System.getProperty("user.home")
247 + File.separatorChar + ".identifiers.org.ids.json";
250 * Allowed values are PDB or mmCIF
252 private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
255 private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
259 * a date formatter using a fixed (rather than the user's) locale;
260 * this ensures that date properties can be written and re-read successfully
261 * even if the user changes their locale setting
263 private static final DateFormat date_format = SimpleDateFormat
264 .getDateTimeInstance(SimpleDateFormat.MEDIUM,
265 SimpleDateFormat.MEDIUM, Locale.UK);
268 * Initialises the Jalview Application Log
270 public static Logger log;
272 /** Jalview Properties */
273 public static Properties applicationProperties = new Properties()
275 // override results in properties output in alphabetical order
277 public synchronized Enumeration<Object> keys()
279 return Collections.enumeration(new TreeSet<>(super.keySet()));
283 /** Default file is ~/.jalview_properties */
284 static String propertiesFile;
286 private static boolean propsAreReadOnly = false;
288 public static void initLogger()
296 // TODO: redirect stdout and stderr here in order to grab the output of
299 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
301 ap.setName("JalviewLogger");
302 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
304 Logger laxis = Logger.getLogger("org.apache.axis");
305 Logger lcastor = Logger.getLogger("org.exolab.castor");
306 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
308 laxis.setLevel(Level.toLevel(
309 Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
310 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
311 Level.INFO.toString())));
312 lcastor = Logger.getLogger("org.exolab.castor.xml");
313 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
314 Level.INFO.toString())));
315 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
316 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
317 // Level.INFO.toString())));
318 // we shouldn't need to do this
319 org.apache.log4j.Logger.getRootLogger()
320 .setLevel(org.apache.log4j.Level.INFO);
322 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
323 .getDefault("logs.Jalview.level", Level.INFO.toString())));
324 // laxis.addAppender(ap);
325 // lcastor.addAppender(ap);
326 // jalview.bin.Cache.log.addAppender(ap);
327 // Tell the user that debug is enabled
328 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
329 } catch (Exception ex)
331 System.err.println("Problems initializing the log4j system\n");
332 ex.printStackTrace(System.err);
337 * Loads properties from the given properties file. Any existing properties
340 public static void loadProperties(String propsFile)
342 propertiesFile = propsFile;
343 if (propsFile == null)
345 propertiesFile = System.getProperty("user.home") + File.separatorChar
346 + ".jalview_properties";
350 // don't corrupt the file we've been given.
351 propsAreReadOnly = true;
359 fis = new java.net.URL(propertiesFile).openStream();
361 "Loading jalview properties from : " + propertiesFile);
363 "Disabling Jalview writing to user's local properties file.");
364 propsAreReadOnly = true;
366 } catch (Exception ex)
372 fis = new FileInputStream(propertiesFile);
374 applicationProperties.clear();
375 applicationProperties.load(fis);
377 // remove any old build properties
379 deleteBuildProperties();
381 } catch (Exception ex)
383 System.out.println("Error reading properties file: " + ex);
386 if (getDefault("USE_PROXY", false))
388 String proxyServer = getDefault("PROXY_SERVER", ""),
389 proxyPort = getDefault("PROXY_PORT", "8080");
391 System.out.println("Using proxyServer: " + proxyServer
392 + " proxyPort: " + proxyPort);
394 System.setProperty("http.proxyHost", proxyServer);
395 System.setProperty("http.proxyPort", proxyPort);
398 // LOAD THE AUTHORS FROM THE authors.props file
401 String authorDetails = "jar:"
402 .concat(Cache.class.getProtectionDomain().getCodeSource()
403 .getLocation().toString().concat("!/authors.props"));
405 java.net.URL localJarFileURL = new java.net.URL(authorDetails);
407 InputStream in = localJarFileURL.openStream();
408 applicationProperties.load(in);
410 } catch (Exception ex)
412 System.out.println("Error reading author details: " + ex);
413 applicationProperties.remove("AUTHORS");
414 applicationProperties.remove("AUTHORFNAMES");
415 applicationProperties.remove("YEAR");
418 loadBuildProperties(false);
421 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
423 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
424 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
426 SiftsSettings.setFailSafePIDThreshold(
427 jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
428 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
430 SiftsSettings.setCacheThresholdInDays(
431 jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
432 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
434 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
435 "https://www.jalview.org/services/identifiers"));
436 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
438 StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
439 .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
440 StructureImportSettings
441 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
442 // StructureImportSettings
443 // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
444 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
446 String jnlpVersion = System.getProperty("jalview.version");
448 // jnlpVersion will be null if a latest version check for the channel needs
450 // Dont do this check if running in headless mode
452 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
453 && (System.getProperty("java.awt.headless") == null || System
454 .getProperty("java.awt.headless").equals("false")))
457 class VersionChecker extends Thread
463 String buildPropertiesUrl = Cache.getAppbaseBuildProperties();
465 String orgtimeout = System
466 .getProperty("sun.net.client.defaultConnectTimeout");
467 if (orgtimeout == null)
470 System.out.println("# INFO: Setting default net timeout to "
471 + orgtimeout + " seconds.");
473 String remoteVersion = null;
476 System.setProperty("sun.net.client.defaultConnectTimeout",
478 java.net.URL url = new java.net.URL(buildPropertiesUrl);
480 BufferedReader in = new BufferedReader(
481 new InputStreamReader(url.openStream()));
483 Properties remoteBuildProperties = new Properties();
484 remoteBuildProperties.load(in);
485 remoteVersion = remoteBuildProperties.getProperty("VERSION");
486 } catch (Exception ex)
489 .println("Non-fatal exception when checking version at "
490 + buildPropertiesUrl + ":");
491 System.out.println(ex);
492 remoteVersion = getProperty("VERSION");
494 System.setProperty("sun.net.client.defaultConnectTimeout",
497 setProperty("LATEST_VERSION", remoteVersion);
501 VersionChecker vc = new VersionChecker();
506 if (jnlpVersion != null)
508 setProperty("LATEST_VERSION", jnlpVersion);
512 applicationProperties.remove("LATEST_VERSION");
516 // LOAD USERDEFINED COLOURS
518 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
519 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
523 public static void loadBuildProperties(boolean reportVersion)
525 String codeInstallation = getProperty("INSTALLATION");
526 boolean printV = codeInstallation == null;
528 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
531 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
532 .getCodeSource().getLocation().toString()
533 .concat("!/.build_properties"));
535 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
537 InputStream in = localJarFileURL.openStream();
538 applicationProperties.load(in);
540 } catch (Exception ex)
542 System.out.println("Error reading build details: " + ex);
543 applicationProperties.remove("VERSION");
545 String codeVersion = getProperty("VERSION");
546 codeInstallation = getProperty("INSTALLATION");
548 if (codeVersion == null)
550 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
551 codeVersion = "Test";
552 codeInstallation = "";
556 codeInstallation = " (" + codeInstallation + ")";
558 setProperty("VERSION", codeVersion);
559 new BuildDetails(codeVersion, null, codeInstallation);
560 if (printV && reportVersion)
563 "Jalview Version: " + codeVersion + codeInstallation);
567 private static void deleteBuildProperties()
569 applicationProperties.remove("LATEST_VERSION");
570 applicationProperties.remove("VERSION");
571 applicationProperties.remove("AUTHORS");
572 applicationProperties.remove("AUTHORFNAMES");
573 applicationProperties.remove("YEAR");
574 applicationProperties.remove("BUILD_DATE");
575 applicationProperties.remove("INSTALLATION");
579 * Gets Jalview application property of given key. Returns null if key not
585 * @return Property value
587 public static String getProperty(String key)
589 return applicationProperties.getProperty(key);
593 * These methods are used when checking if the saved preference is different
594 * to the default setting
597 public static boolean getDefault(String property, boolean def)
599 String string = getProperty(property);
602 def = Boolean.valueOf(string).booleanValue();
608 public static int getDefault(String property, int def)
610 String string = getProperty(property);
615 def = Integer.parseInt(string);
616 } catch (NumberFormatException e)
618 System.out.println("Error parsing int property '" + property
619 + "' with value '" + string + "'");
627 * These methods are used when checking if the saved preference is different
628 * to the default setting
630 public static String getDefault(String property, String def)
632 String string = getProperty(property);
642 * Stores property in the file "HOME_DIR/.jalview_properties"
647 * String value of property
649 * @return previous value of property (or null)
651 public static Object setProperty(String key, String obj)
653 Object oldValue = null;
656 oldValue = applicationProperties.setProperty(key, obj);
657 if (propertiesFile != null && !propsAreReadOnly)
659 FileOutputStream out = new FileOutputStream(propertiesFile);
660 applicationProperties.store(out, "---JalviewX Properties File---");
663 } catch (Exception ex)
666 "Error setting property: " + key + " " + obj + "\n" + ex);
672 * remove the specified property from the jalview properties file
676 public static void removeProperty(String string)
678 applicationProperties.remove(string);
683 * save the properties to the jalview properties path
685 public static void saveProperties()
687 if (!propsAreReadOnly)
691 FileOutputStream out = new FileOutputStream(propertiesFile);
692 applicationProperties.store(out, "---JalviewX Properties File---");
694 } catch (Exception ex)
696 System.out.println("Error saving properties: " + ex);
702 * internal vamsas class discovery state
704 private static int vamsasJarsArePresent = -1;
707 * Searches for vamsas client classes on class path.
709 * @return true if vamsas client is present on classpath
711 public static boolean vamsasJarsPresent()
713 if (vamsasJarsArePresent == -1)
717 if (jalview.jbgui.GDesktop.class.getClassLoader()
718 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
720 jalview.bin.Cache.log.debug(
721 "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
722 vamsasJarsArePresent = 1;
723 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
724 lvclient.setLevel(Level.toLevel(Cache
725 .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
727 lvclient.addAppender(log.getAppender("JalviewLogger"));
728 // Tell the user that debug is enabled
729 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
731 } catch (Exception e)
733 vamsasJarsArePresent = 0;
734 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
737 return (vamsasJarsArePresent > 0);
741 * internal vamsas class discovery state
743 private static int groovyJarsArePresent = -1;
746 * Searches for vamsas client classes on class path.
748 * @return true if vamsas client is present on classpath
750 public static boolean groovyJarsPresent()
752 if (groovyJarsArePresent == -1)
756 if (Cache.class.getClassLoader()
757 .loadClass("groovy.lang.GroovyObject") != null)
759 jalview.bin.Cache.log.debug(
760 "Found Groovy (groovy.lang.GroovyObject can be loaded)");
761 groovyJarsArePresent = 1;
762 Logger lgclient = Logger.getLogger("groovy");
763 lgclient.setLevel(Level.toLevel(Cache
764 .getDefault("logs.Groovy.Level", Level.INFO.toString())));
766 lgclient.addAppender(log.getAppender("JalviewLogger"));
767 // Tell the user that debug is enabled
768 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
772 groovyJarsArePresent = 0;
773 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
774 } catch (Exception e)
776 groovyJarsArePresent = 0;
777 jalview.bin.Cache.log.debug("Groovy Classes are not present");
780 return (groovyJarsArePresent > 0);
784 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
787 protected static Object tracker = null;
789 protected static Class trackerfocus = null;
791 protected static Class jgoogleanalyticstracker = null;
794 * Initialise the google tracker if it is not done already.
796 public static void initGoogleTracker()
800 if (jgoogleanalyticstracker == null)
802 // try to get the tracker class
805 jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
806 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
807 trackerfocus = Cache.class.getClassLoader()
808 .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
809 } catch (Exception e)
812 "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
814 jgoogleanalyticstracker = null;
819 // now initialise tracker
820 Exception re = null, ex = null;
822 String vrs = "No Version Accessible";
825 // Google analytics tracking code for Library Finder
826 tracker = jgoogleanalyticstracker
827 .getConstructor(new Class[]
828 { String.class, String.class, String.class })
829 .newInstance(new Object[]
831 (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
832 + jalview.bin.Cache.getDefault("BUILD_DATE",
835 jgoogleanalyticstracker
836 .getMethod("trackAsynchronously", new Class[]
838 .invoke(tracker, new Object[]
839 { trackerfocus.getConstructor(new Class[] { String.class })
840 .newInstance(new Object[]
841 { "Application Started." }) });
842 } catch (RuntimeException e)
845 } catch (Exception e)
852 if (re != null || ex != null || err != null)
858 log.debug("Caught runtime exception in googletracker init:",
864 "Failed to initialise GoogleTracker for Jalview Desktop with version "
871 "Whilst initing GoogleTracker for Jalview Desktop version "
881 "Debug: Caught runtime exception in googletracker init:"
883 re.printStackTrace();
888 "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
890 ex.printStackTrace();
896 "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
898 err.printStackTrace();
904 log.debug("Successfully initialised tracker.");
910 * get the user's default colour if available
916 public static Color getDefaultColour(String property, Color defcolour)
918 String colprop = getProperty(property);
923 Color col = ColorUtils.parseColourString(colprop);
926 log.warn("Couldn't parse '" + colprop + "' as a colour for "
929 return (col == null) ? defcolour : col;
933 * store a colour as a Jalview user default property
938 public static void setColourProperty(String property, Color colour)
940 setProperty(property, jalview.util.Format.getHexString(colour));
944 * Stores a formatted date in a jalview property, using a fixed locale.
946 * @param propertyName
948 * @return the formatted date string
950 public static String setDateProperty(String propertyName, Date date)
952 String formatted = date_format.format(date);
953 setProperty(propertyName, formatted);
958 * Reads a date stored in a Jalview property, parses it (using a fixed locale
959 * format) and returns as a Date, or null if parsing fails
961 * @param propertyName
965 public static Date getDateProperty(String propertyName)
967 String val = getProperty(propertyName);
972 return date_format.parse(val);
973 } catch (Exception ex)
975 System.err.println("Invalid or corrupt date in property '"
976 + propertyName + "' : value was '" + val + "'");
983 * get and parse a property as an integer. send any parsing problems to
987 * @return null or Integer
989 public static Integer getIntegerProperty(String property)
991 String val = getProperty(property);
992 if (val != null && (val = val.trim()).length() > 0)
996 return Integer.valueOf(val);
997 } catch (NumberFormatException x)
999 System.err.println("Invalid integer in property '" + property
1000 + "' (value was '" + val + "')");
1007 * Set the specified value, or remove it if null or empty. Does not save the
1013 public static void setOrRemove(String propName, String value)
1015 if (propName == null)
1019 if (value == null || value.trim().length() < 1)
1021 Cache.applicationProperties.remove(propName);
1025 Cache.applicationProperties.setProperty(propName, value);
1030 * Loads in user colour schemes from files.
1033 * a '|'-delimited list of file paths
1035 public static void initUserColourSchemes(String files)
1037 if (files == null || files.length() == 0)
1042 // In case colours can't be loaded, we'll remove them
1043 // from the default list here.
1044 StringBuffer coloursFound = new StringBuffer();
1045 StringTokenizer st = new StringTokenizer(files, "|");
1046 while (st.hasMoreElements())
1048 String file = st.nextToken();
1051 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1054 if (coloursFound.length() > 0)
1056 coloursFound.append("|");
1058 coloursFound.append(file);
1059 ColourSchemes.getInstance().registerColourScheme(ucs);
1061 } catch (Exception ex)
1063 System.out.println("Error loading User ColourFile\n" + ex);
1066 if (!files.equals(coloursFound.toString()))
1068 if (coloursFound.toString().length() > 1)
1070 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1071 coloursFound.toString());
1075 applicationProperties
1076 .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1082 * Initial logging information helper for various versions output
1086 * @param defaultValue
1088 private static void appendIfNotNull(StringBuilder sb, String prefix,
1089 String value, String suffix, String defaultValue)
1091 if (value == null && defaultValue == null)
1095 String line = prefix + (value != null ? value : defaultValue) + suffix;
1101 * @return Jalview version, build details and JVM platform version for console
1103 public static String getVersionDetailsForConsole()
1105 StringBuilder sb = new StringBuilder();
1106 sb.append("Jalview Version: ");
1107 sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
1109 sb.append("Jalview Installation: ");
1110 sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
1112 sb.append("Build Date: ");
1113 sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
1115 sb.append("Java version: ");
1116 sb.append(System.getProperty("java.version"));
1118 sb.append(System.getProperty("os.arch"));
1120 sb.append(System.getProperty("os.name"));
1122 sb.append(System.getProperty("os.version"));
1124 appendIfNotNull(sb, "Install4j version: ",
1125 System.getProperty("sys.install4jVersion"), "\n", null);
1126 appendIfNotNull(sb, "Install4j template version: ",
1127 System.getProperty("installer_template_version"), "\n", null);
1128 appendIfNotNull(sb, "Launcher version: ",
1129 System.getProperty("launcher_version"), "\n", null);
1130 LookAndFeel laf = UIManager.getLookAndFeel();
1131 String lafName = laf == null ? "Not obtained" : laf.getName();
1132 String lafClass = laf == null ? "unknown" : laf.getClass().getName();
1133 sb.append("LookAndFeel: ");
1136 sb.append(lafClass);
1138 // Not displayed in release version ( determined by possible version number
1139 // regex 9[9.]*9[.-_a9]* )
1140 if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
1141 jalview.bin.Cache.getDefault("VERSION", "TEST")))
1143 appendIfNotNull(sb, "Getdown appdir: ",
1144 System.getProperty("getdownappdir"), "\n", null);
1145 appendIfNotNull(sb, "Getdown appbase: ",
1146 System.getProperty("getdownappbase"), "\n", null);
1147 appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
1150 return sb.toString();
1155 * @return build details as reported in splashscreen
1157 public static String getBuildDetailsForSplash()
1159 // consider returning more human friendly info
1160 // eg 'built from Source' or update channel
1161 return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
1164 public static String getStackTraceString(Throwable t)
1166 StringWriter sw = new StringWriter();
1167 PrintWriter pw = new PrintWriter(sw);
1168 t.printStackTrace(pw);
1169 return sw.toString();
1173 * Getdown appbase methods
1176 private static final String releaseAppbase;
1178 private static String getdownAppbase;
1180 private static String getdownDistDir;
1184 Float specversion = Float
1185 .parseFloat(System.getProperty("java.specification.version"));
1186 releaseAppbase = (specversion < 9)
1187 ? "https://www.jalview.org/getdown/release/1.8"
1188 : "https://www.jalview.org/getdown/release/11";
1191 // look for properties (passed in by getdown) otherwise default to release
1192 private static void setGetdownAppbase()
1194 if (getdownAppbase != null)
1198 String appbase = System.getProperty("getdownappbase");
1199 String distDir = System.getProperty("getdowndistdir");
1200 if (appbase == null)
1202 appbase = releaseAppbase;
1203 distDir = "release";
1205 if (appbase.endsWith("/"))
1207 appbase = appbase.substring(0, appbase.length() - 1);
1209 if (distDir == null)
1211 distDir = appbase.equals(releaseAppbase) ? "release" : "alt";
1213 getdownAppbase = appbase;
1214 getdownDistDir = distDir;
1217 public static String getGetdownAppbase()
1219 setGetdownAppbase();
1220 return getdownAppbase;
1223 public static String getAppbaseBuildProperties()
1225 String appbase = getGetdownAppbase();
1226 return appbase + "/" + getdownDistDir + "/build_properties";