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
198 * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
200 * Deprecated settings:
203 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
204 * startup (JWS1 services only)</li>
205 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
206 * (JWS1 services only)</li>
207 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
208 * services in the desktop GUI</li>
209 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
210 * panel in web service preferences</li>
214 * @version $Revision$
219 * property giving log4j level for CASTOR loggers
221 public static final String CASTORLOGLEVEL = "logs.Castor.level";
224 * property giving log4j level for AXIS loggers
226 public static final String AXISLOGLEVEL = "logs.Axis.level";
229 * property giving log4j level for Jalview Log
231 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
236 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
237 .getProperty("user.home") + File.separatorChar
238 + ".sifts_downloads" + File.separatorChar;
240 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
242 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
245 * Identifiers.org download settings
247 private static final String ID_ORG_FILE = System.getProperty("user.home")
248 + File.separatorChar + ".identifiers.org.ids.json";
251 * Allowed values are PDB or mmCIF
253 private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
256 private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
260 * a date formatter using a fixed (rather than the user's) locale;
261 * this ensures that date properties can be written and re-read successfully
262 * even if the user changes their locale setting
264 private static final DateFormat date_format = SimpleDateFormat
265 .getDateTimeInstance(SimpleDateFormat.MEDIUM,
266 SimpleDateFormat.MEDIUM, Locale.UK);
269 * Initialises the Jalview Application Log
271 public static Logger log;
273 /** Jalview Properties */
274 public static Properties applicationProperties = new Properties()
276 // override results in properties output in alphabetical order
278 public synchronized Enumeration<Object> keys()
280 return Collections.enumeration(new TreeSet<>(super.keySet()));
284 /** Default file is ~/.jalview_properties */
285 static String propertiesFile;
287 private static boolean propsAreReadOnly = false;
289 public static void initLogger()
297 // TODO: redirect stdout and stderr here in order to grab the output of
300 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
302 ap.setName("JalviewLogger");
303 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
305 Logger laxis = Logger.getLogger("org.apache.axis");
306 Logger lcastor = Logger.getLogger("org.exolab.castor");
307 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
309 laxis.setLevel(Level.toLevel(
310 Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
311 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
312 Level.INFO.toString())));
313 lcastor = Logger.getLogger("org.exolab.castor.xml");
314 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
315 Level.INFO.toString())));
316 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
317 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
318 // Level.INFO.toString())));
319 // we shouldn't need to do this
320 org.apache.log4j.Logger.getRootLogger()
321 .setLevel(org.apache.log4j.Level.INFO);
323 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
324 .getDefault("logs.Jalview.level", Level.INFO.toString())));
325 // laxis.addAppender(ap);
326 // lcastor.addAppender(ap);
327 // jalview.bin.Cache.log.addAppender(ap);
328 // Tell the user that debug is enabled
329 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
330 } catch (Exception ex)
332 System.err.println("Problems initializing the log4j system\n");
333 ex.printStackTrace(System.err);
338 * Loads properties from the given properties file. Any existing properties
341 public static void loadProperties(String propsFile)
343 propertiesFile = propsFile;
344 if (propsFile == null)
346 propertiesFile = System.getProperty("user.home") + File.separatorChar
347 + ".jalview_properties";
351 // don't corrupt the file we've been given.
352 propsAreReadOnly = true;
360 fis = new java.net.URL(propertiesFile).openStream();
362 "Loading jalview properties from : " + propertiesFile);
364 "Disabling Jalview writing to user's local properties file.");
365 propsAreReadOnly = true;
367 } catch (Exception ex)
373 fis = new FileInputStream(propertiesFile);
375 applicationProperties.clear();
376 applicationProperties.load(fis);
378 // remove any old build properties
380 deleteBuildProperties();
382 } catch (Exception ex)
384 System.out.println("Error reading properties file: " + ex);
387 if (getDefault("USE_PROXY", false))
389 String proxyServer = getDefault("PROXY_SERVER", ""),
390 proxyPort = getDefault("PROXY_PORT", "8080");
392 System.out.println("Using proxyServer: " + proxyServer
393 + " proxyPort: " + proxyPort);
395 System.setProperty("http.proxyHost", proxyServer);
396 System.setProperty("http.proxyPort", proxyPort);
399 // LOAD THE AUTHORS FROM THE authors.props file
402 String authorDetails = "jar:"
403 .concat(Cache.class.getProtectionDomain().getCodeSource()
404 .getLocation().toString().concat("!/authors.props"));
406 java.net.URL localJarFileURL = new java.net.URL(authorDetails);
408 InputStream in = localJarFileURL.openStream();
409 applicationProperties.load(in);
411 } catch (Exception ex)
413 System.out.println("Error reading author details: " + ex);
414 applicationProperties.remove("AUTHORS");
415 applicationProperties.remove("AUTHORFNAMES");
416 applicationProperties.remove("YEAR");
419 loadBuildProperties(false);
422 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
424 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
425 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
427 SiftsSettings.setFailSafePIDThreshold(
428 jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
429 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
431 SiftsSettings.setCacheThresholdInDays(
432 jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
433 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
435 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
436 "https://www.jalview.org/services/identifiers"));
437 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
439 StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
440 .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
441 StructureImportSettings
442 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
443 // StructureImportSettings
444 // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
445 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
447 String jnlpVersion = System.getProperty("jalview.version");
449 // jnlpVersion will be null if a latest version check for the channel needs
451 // Dont do this check if running in headless mode
453 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
454 && (System.getProperty("java.awt.headless") == null || System
455 .getProperty("java.awt.headless").equals("false")))
458 class VersionChecker extends Thread
464 String buildPropertiesUrl = Cache.getAppbaseBuildProperties();
466 String orgtimeout = System
467 .getProperty("sun.net.client.defaultConnectTimeout");
468 if (orgtimeout == null)
471 System.out.println("# INFO: Setting default net timeout to "
472 + orgtimeout + " seconds.");
474 String remoteVersion = null;
477 System.setProperty("sun.net.client.defaultConnectTimeout",
479 java.net.URL url = new java.net.URL(buildPropertiesUrl);
481 BufferedReader in = new BufferedReader(
482 new InputStreamReader(url.openStream()));
484 Properties remoteBuildProperties = new Properties();
485 remoteBuildProperties.load(in);
486 remoteVersion = remoteBuildProperties.getProperty("VERSION");
487 } catch (Exception ex)
490 .println("Non-fatal exception when checking version at "
491 + buildPropertiesUrl + ":");
492 System.out.println(ex);
493 remoteVersion = getProperty("VERSION");
495 System.setProperty("sun.net.client.defaultConnectTimeout",
498 setProperty("LATEST_VERSION", remoteVersion);
502 VersionChecker vc = new VersionChecker();
507 if (jnlpVersion != null)
509 setProperty("LATEST_VERSION", jnlpVersion);
513 applicationProperties.remove("LATEST_VERSION");
517 // LOAD USERDEFINED COLOURS
519 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
520 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
524 public static void loadBuildProperties(boolean reportVersion)
526 String codeInstallation = getProperty("INSTALLATION");
527 boolean printV = codeInstallation == null;
529 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
532 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
533 .getCodeSource().getLocation().toString()
534 .concat("!/.build_properties"));
536 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
538 InputStream in = localJarFileURL.openStream();
539 applicationProperties.load(in);
541 } catch (Exception ex)
543 System.out.println("Error reading build details: " + ex);
544 applicationProperties.remove("VERSION");
546 String codeVersion = getProperty("VERSION");
547 codeInstallation = getProperty("INSTALLATION");
549 if (codeVersion == null)
551 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
552 codeVersion = "Test";
553 codeInstallation = "";
557 codeInstallation = " (" + codeInstallation + ")";
559 setProperty("VERSION", codeVersion);
560 new BuildDetails(codeVersion, null, codeInstallation);
561 if (printV && reportVersion)
564 "Jalview Version: " + codeVersion + codeInstallation);
568 private static void deleteBuildProperties()
570 applicationProperties.remove("LATEST_VERSION");
571 applicationProperties.remove("VERSION");
572 applicationProperties.remove("AUTHORS");
573 applicationProperties.remove("AUTHORFNAMES");
574 applicationProperties.remove("YEAR");
575 applicationProperties.remove("BUILD_DATE");
576 applicationProperties.remove("INSTALLATION");
580 * Gets Jalview application property of given key. Returns null if key not
586 * @return Property value
588 public static String getProperty(String key)
590 return applicationProperties.getProperty(key);
594 * These methods are used when checking if the saved preference is different
595 * to the default setting
598 public static boolean getDefault(String property, boolean def)
600 String string = getProperty(property);
603 def = Boolean.valueOf(string).booleanValue();
609 public static int getDefault(String property, int def)
611 String string = getProperty(property);
616 def = Integer.parseInt(string);
617 } catch (NumberFormatException e)
619 System.out.println("Error parsing int property '" + property
620 + "' with value '" + string + "'");
628 * These methods are used when checking if the saved preference is different
629 * to the default setting
631 public static String getDefault(String property, String def)
633 String string = getProperty(property);
643 * Stores property in the file "HOME_DIR/.jalview_properties"
648 * String value of property
650 * @return previous value of property (or null)
652 public static Object setProperty(String key, String obj)
654 Object oldValue = null;
657 oldValue = applicationProperties.setProperty(key, obj);
658 if (propertiesFile != null && !propsAreReadOnly)
660 FileOutputStream out = new FileOutputStream(propertiesFile);
661 applicationProperties.store(out, "---JalviewX Properties File---");
664 } catch (Exception ex)
667 "Error setting property: " + key + " " + obj + "\n" + ex);
673 * remove the specified property from the jalview properties file
677 public static void removeProperty(String string)
679 applicationProperties.remove(string);
684 * save the properties to the jalview properties path
686 public static void saveProperties()
688 if (!propsAreReadOnly)
692 FileOutputStream out = new FileOutputStream(propertiesFile);
693 applicationProperties.store(out, "---JalviewX Properties File---");
695 } catch (Exception ex)
697 System.out.println("Error saving properties: " + ex);
703 * internal vamsas class discovery state
705 private static int vamsasJarsArePresent = -1;
708 * Searches for vamsas client classes on class path.
710 * @return true if vamsas client is present on classpath
712 public static boolean vamsasJarsPresent()
714 if (vamsasJarsArePresent == -1)
718 if (jalview.jbgui.GDesktop.class.getClassLoader()
719 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
721 jalview.bin.Cache.log.debug(
722 "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
723 vamsasJarsArePresent = 1;
724 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
725 lvclient.setLevel(Level.toLevel(Cache
726 .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
728 lvclient.addAppender(log.getAppender("JalviewLogger"));
729 // Tell the user that debug is enabled
730 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
732 } catch (Exception e)
734 vamsasJarsArePresent = 0;
735 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
738 return (vamsasJarsArePresent > 0);
742 * internal vamsas class discovery state
744 private static int groovyJarsArePresent = -1;
747 * Searches for vamsas client classes on class path.
749 * @return true if vamsas client is present on classpath
751 public static boolean groovyJarsPresent()
753 if (groovyJarsArePresent == -1)
757 if (Cache.class.getClassLoader()
758 .loadClass("groovy.lang.GroovyObject") != null)
760 jalview.bin.Cache.log.debug(
761 "Found Groovy (groovy.lang.GroovyObject can be loaded)");
762 groovyJarsArePresent = 1;
763 Logger lgclient = Logger.getLogger("groovy");
764 lgclient.setLevel(Level.toLevel(Cache
765 .getDefault("logs.Groovy.Level", Level.INFO.toString())));
767 lgclient.addAppender(log.getAppender("JalviewLogger"));
768 // Tell the user that debug is enabled
769 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
773 groovyJarsArePresent = 0;
774 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
775 } catch (Exception e)
777 groovyJarsArePresent = 0;
778 jalview.bin.Cache.log.debug("Groovy Classes are not present");
781 return (groovyJarsArePresent > 0);
785 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
788 protected static Object tracker = null;
790 protected static Class trackerfocus = null;
792 protected static Class jgoogleanalyticstracker = null;
795 * Initialise the google tracker if it is not done already.
797 public static void initGoogleTracker()
801 if (jgoogleanalyticstracker == null)
803 // try to get the tracker class
806 jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
807 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
808 trackerfocus = Cache.class.getClassLoader()
809 .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
810 } catch (Exception e)
813 "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
815 jgoogleanalyticstracker = null;
820 // now initialise tracker
821 Exception re = null, ex = null;
823 String vrs = "No Version Accessible";
826 // Google analytics tracking code for Library Finder
827 tracker = jgoogleanalyticstracker
828 .getConstructor(new Class[]
829 { String.class, String.class, String.class })
830 .newInstance(new Object[]
832 (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
833 + jalview.bin.Cache.getDefault("BUILD_DATE",
836 jgoogleanalyticstracker
837 .getMethod("trackAsynchronously", new Class[]
839 .invoke(tracker, new Object[]
840 { trackerfocus.getConstructor(new Class[] { String.class })
841 .newInstance(new Object[]
842 { "Application Started." }) });
843 } catch (RuntimeException e)
846 } catch (Exception e)
853 if (re != null || ex != null || err != null)
859 log.debug("Caught runtime exception in googletracker init:",
865 "Failed to initialise GoogleTracker for Jalview Desktop with version "
872 "Whilst initing GoogleTracker for Jalview Desktop version "
882 "Debug: Caught runtime exception in googletracker init:"
884 re.printStackTrace();
889 "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
891 ex.printStackTrace();
897 "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
899 err.printStackTrace();
905 log.debug("Successfully initialised tracker.");
911 * get the user's default colour if available
917 public static Color getDefaultColour(String property, Color defcolour)
919 String colprop = getProperty(property);
924 Color col = ColorUtils.parseColourString(colprop);
927 log.warn("Couldn't parse '" + colprop + "' as a colour for "
930 return (col == null) ? defcolour : col;
934 * store a colour as a Jalview user default property
939 public static void setColourProperty(String property, Color colour)
941 setProperty(property, jalview.util.Format.getHexString(colour));
945 * Stores a formatted date in a jalview property, using a fixed locale.
947 * @param propertyName
949 * @return the formatted date string
951 public static String setDateProperty(String propertyName, Date date)
953 String formatted = date_format.format(date);
954 setProperty(propertyName, formatted);
959 * Reads a date stored in a Jalview property, parses it (using a fixed locale
960 * format) and returns as a Date, or null if parsing fails
962 * @param propertyName
966 public static Date getDateProperty(String propertyName)
968 String val = getProperty(propertyName);
973 return date_format.parse(val);
974 } catch (Exception ex)
976 System.err.println("Invalid or corrupt date in property '"
977 + propertyName + "' : value was '" + val + "'");
984 * get and parse a property as an integer. send any parsing problems to
988 * @return null or Integer
990 public static Integer getIntegerProperty(String property)
992 String val = getProperty(property);
993 if (val != null && (val = val.trim()).length() > 0)
997 return Integer.valueOf(val);
998 } catch (NumberFormatException x)
1000 System.err.println("Invalid integer in property '" + property
1001 + "' (value was '" + val + "')");
1008 * Set the specified value, or remove it if null or empty. Does not save the
1014 public static void setOrRemove(String propName, String value)
1016 if (propName == null)
1020 if (value == null || value.trim().length() < 1)
1022 Cache.applicationProperties.remove(propName);
1026 Cache.applicationProperties.setProperty(propName, value);
1031 * Loads in user colour schemes from files.
1034 * a '|'-delimited list of file paths
1036 public static void initUserColourSchemes(String files)
1038 if (files == null || files.length() == 0)
1043 // In case colours can't be loaded, we'll remove them
1044 // from the default list here.
1045 StringBuffer coloursFound = new StringBuffer();
1046 StringTokenizer st = new StringTokenizer(files, "|");
1047 while (st.hasMoreElements())
1049 String file = st.nextToken();
1052 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1055 if (coloursFound.length() > 0)
1057 coloursFound.append("|");
1059 coloursFound.append(file);
1060 ColourSchemes.getInstance().registerColourScheme(ucs);
1062 } catch (Exception ex)
1064 System.out.println("Error loading User ColourFile\n" + ex);
1067 if (!files.equals(coloursFound.toString()))
1069 if (coloursFound.toString().length() > 1)
1071 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1072 coloursFound.toString());
1076 applicationProperties
1077 .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1083 * Initial logging information helper for various versions output
1087 * @param defaultValue
1089 private static void appendIfNotNull(StringBuilder sb, String prefix,
1090 String value, String suffix, String defaultValue)
1092 if (value == null && defaultValue == null)
1096 String line = prefix + (value != null ? value : defaultValue) + suffix;
1102 * @return Jalview version, build details and JVM platform version for console
1104 public static String getVersionDetailsForConsole()
1106 StringBuilder sb = new StringBuilder();
1107 sb.append("Jalview Version: ");
1108 sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
1110 sb.append("Jalview Installation: ");
1111 sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
1113 sb.append("Build Date: ");
1114 sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
1116 sb.append("Java version: ");
1117 sb.append(System.getProperty("java.version"));
1119 sb.append(System.getProperty("os.arch"));
1121 sb.append(System.getProperty("os.name"));
1123 sb.append(System.getProperty("os.version"));
1125 appendIfNotNull(sb, "Install4j version: ",
1126 System.getProperty("sys.install4jVersion"), "\n", null);
1127 appendIfNotNull(sb, "Install4j template version: ",
1128 System.getProperty("installer_template_version"), "\n", null);
1129 appendIfNotNull(sb, "Launcher version: ",
1130 System.getProperty("launcher_version"), "\n", null);
1131 LookAndFeel laf = UIManager.getLookAndFeel();
1132 String lafName = laf == null ? "Not obtained" : laf.getName();
1133 String lafClass = laf == null ? "unknown" : laf.getClass().getName();
1134 sb.append("LookAndFeel: ");
1137 sb.append(lafClass);
1139 // Not displayed in release version ( determined by possible version number
1140 // regex 9[9.]*9[.-_a9]* )
1141 if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
1142 jalview.bin.Cache.getDefault("VERSION", "TEST")))
1144 appendIfNotNull(sb, "Getdown appdir: ",
1145 System.getProperty("getdownappdir"), "\n", null);
1146 appendIfNotNull(sb, "Getdown appbase: ",
1147 System.getProperty("getdownappbase"), "\n", null);
1148 appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
1151 return sb.toString();
1156 * @return build details as reported in splashscreen
1158 public static String getBuildDetailsForSplash()
1160 // consider returning more human friendly info
1161 // eg 'built from Source' or update channel
1162 return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
1165 public static String getStackTraceString(Throwable t)
1167 StringWriter sw = new StringWriter();
1168 PrintWriter pw = new PrintWriter(sw);
1169 t.printStackTrace(pw);
1170 return sw.toString();
1174 * Getdown appbase methods
1177 private static final String releaseAppbase;
1179 private static String getdownAppbase;
1181 private static String getdownDistDir;
1185 Float specversion = Float
1186 .parseFloat(System.getProperty("java.specification.version"));
1187 releaseAppbase = (specversion < 9)
1188 ? "https://www.jalview.org/getdown/release/1.8"
1189 : "https://www.jalview.org/getdown/release/11";
1192 // look for properties (passed in by getdown) otherwise default to release
1193 private static void setGetdownAppbase()
1195 if (getdownAppbase != null)
1199 String appbase = System.getProperty("getdownappbase");
1200 String distDir = System.getProperty("getdowndistdir");
1201 if (appbase == null)
1203 appbase = releaseAppbase;
1204 distDir = "release";
1206 if (appbase.endsWith("/"))
1208 appbase = appbase.substring(0, appbase.length() - 1);
1210 if (distDir == null)
1212 distDir = appbase.equals(releaseAppbase) ? "release" : "alt";
1214 getdownAppbase = appbase;
1215 getdownDistDir = distDir;
1218 public static String getGetdownAppbase()
1220 setGetdownAppbase();
1221 return getdownAppbase;
1224 public static String getAppbaseBuildProperties()
1226 String appbase = getGetdownAppbase();
1227 return appbase + "/" + getdownDistDir + "/build_properties";