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>SHOW_JWS2_SERVICES (true) when set to false, jalview will not
171 * auto-discover JABAWS services</li>
172 * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
173 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
174 * warning dialog box is displayed.</li>
175 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
176 * when shading by annotation</li>
177 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
178 * when shading by annotation</li>
179 * <li>www.jalview.org (https://www.jalview.org) a property enabling all HTTP
180 * requests to be redirected to a mirror of https://www.jalview.org</li>
181 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
182 * alignment figure to accommodate even the longest sequence ID or annotation
184 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
185 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
186 * will override this).</li>
187 * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
189 * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
190 * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
192 * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
194 * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
196 * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
197 * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
200 * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
201 * <li>NOHTMLTEMPLATES - when set, the
202 * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
203 * not downloaded automatically</li>
205 * Deprecated settings:
208 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
209 * startup (JWS1 services only)</li>
210 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
211 * (JWS1 services only)</li>
212 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
213 * services in the desktop GUI</li>
214 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
215 * panel in web service preferences</li>
219 * @version $Revision$
224 * property giving log4j level for CASTOR loggers
226 public static final String CASTORLOGLEVEL = "logs.Castor.level";
229 * property giving log4j level for AXIS loggers
231 public static final String AXISLOGLEVEL = "logs.Axis.level";
234 * property giving log4j level for Jalview Log
236 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
241 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
242 .getProperty("user.home") + File.separatorChar
243 + ".sifts_downloads" + File.separatorChar;
245 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
247 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
250 * Identifiers.org download settings
252 private static final String ID_ORG_FILE = System.getProperty("user.home")
253 + File.separatorChar + ".identifiers.org.ids.json";
256 * Allowed values are PDB or mmCIF
258 private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
261 private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
265 * a date formatter using a fixed (rather than the user's) locale;
266 * this ensures that date properties can be written and re-read successfully
267 * even if the user changes their locale setting
269 private static final DateFormat date_format = SimpleDateFormat
270 .getDateTimeInstance(SimpleDateFormat.MEDIUM,
271 SimpleDateFormat.MEDIUM, Locale.UK);
274 * Initialises the Jalview Application Log
276 public static Logger log;
278 /** Jalview Properties */
279 public static Properties applicationProperties = new Properties()
281 // override results in properties output in alphabetical order
283 public synchronized Enumeration<Object> keys()
285 return Collections.enumeration(new TreeSet<>(super.keySet()));
289 /** Default file is ~/.jalview_properties */
290 static String propertiesFile;
292 private static boolean propsAreReadOnly = false;
294 public static void initLogger()
302 // TODO: redirect stdout and stderr here in order to grab the output of
305 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
307 ap.setName("JalviewLogger");
308 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
310 Logger laxis = Logger.getLogger("org.apache.axis");
311 Logger lcastor = Logger.getLogger("org.exolab.castor");
312 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
314 laxis.setLevel(Level.toLevel(
315 Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
316 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
317 Level.INFO.toString())));
318 lcastor = Logger.getLogger("org.exolab.castor.xml");
319 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
320 Level.INFO.toString())));
321 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
322 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
323 // Level.INFO.toString())));
324 // we shouldn't need to do this
325 org.apache.log4j.Logger.getRootLogger()
326 .setLevel(org.apache.log4j.Level.INFO);
328 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
329 .getDefault("logs.Jalview.level", Level.INFO.toString())));
330 // laxis.addAppender(ap);
331 // lcastor.addAppender(ap);
332 // jalview.bin.Cache.log.addAppender(ap);
333 // Tell the user that debug is enabled
334 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
335 } catch (Exception ex)
337 System.err.println("Problems initializing the log4j system\n");
338 ex.printStackTrace(System.err);
343 * Loads properties from the given properties file. Any existing properties
346 public static void loadProperties(String propsFile)
348 propertiesFile = propsFile;
349 if (propsFile == null)
351 propertiesFile = System.getProperty("user.home") + File.separatorChar
352 + ".jalview_properties";
356 // don't corrupt the file we've been given.
357 propsAreReadOnly = true;
365 fis = new java.net.URL(propertiesFile).openStream();
367 "Loading jalview properties from : " + propertiesFile);
369 "Disabling Jalview writing to user's local properties file.");
370 propsAreReadOnly = true;
372 } catch (Exception ex)
378 fis = new FileInputStream(propertiesFile);
380 applicationProperties.clear();
381 applicationProperties.load(fis);
383 // remove any old build properties
385 deleteBuildProperties();
387 } catch (Exception ex)
389 System.out.println("Error reading properties file: " + ex);
392 if (getDefault("USE_PROXY", false))
394 String proxyServer = getDefault("PROXY_SERVER", ""),
395 proxyPort = getDefault("PROXY_PORT", "8080");
397 System.out.println("Using proxyServer: " + proxyServer
398 + " proxyPort: " + proxyPort);
400 System.setProperty("http.proxyHost", proxyServer);
401 System.setProperty("http.proxyPort", proxyPort);
404 // LOAD THE AUTHORS FROM THE authors.props file
407 String authorDetails = "jar:"
408 .concat(Cache.class.getProtectionDomain().getCodeSource()
409 .getLocation().toString().concat("!/authors.props"));
411 java.net.URL localJarFileURL = new java.net.URL(authorDetails);
413 InputStream in = localJarFileURL.openStream();
414 applicationProperties.load(in);
416 } catch (Exception ex)
418 System.out.println("Error reading author details: " + ex);
419 applicationProperties.remove("AUTHORS");
420 applicationProperties.remove("AUTHORFNAMES");
421 applicationProperties.remove("YEAR");
424 loadBuildProperties(false);
427 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
429 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
430 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
432 SiftsSettings.setFailSafePIDThreshold(
433 jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
434 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
436 SiftsSettings.setCacheThresholdInDays(
437 jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
438 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
440 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
441 "https://www.jalview.org/services/identifiers"));
442 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
444 StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
445 .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
446 StructureImportSettings
447 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
448 // StructureImportSettings
449 // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
450 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
452 String jnlpVersion = System.getProperty("jalview.version");
454 // jnlpVersion will be null if a latest version check for the channel needs
456 // Dont do this check if running in headless mode
458 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
459 && (System.getProperty("java.awt.headless") == null || System
460 .getProperty("java.awt.headless").equals("false")))
463 class VersionChecker extends Thread
469 String buildPropertiesUrl = Cache.getAppbaseBuildProperties();
471 String orgtimeout = System
472 .getProperty("sun.net.client.defaultConnectTimeout");
473 if (orgtimeout == null)
476 System.out.println("# INFO: Setting default net timeout to "
477 + orgtimeout + " seconds.");
479 String remoteVersion = null;
482 System.setProperty("sun.net.client.defaultConnectTimeout",
484 java.net.URL url = new java.net.URL(buildPropertiesUrl);
486 BufferedReader in = new BufferedReader(
487 new InputStreamReader(url.openStream()));
489 Properties remoteBuildProperties = new Properties();
490 remoteBuildProperties.load(in);
491 remoteVersion = remoteBuildProperties.getProperty("VERSION");
492 } catch (Exception ex)
495 .println("Non-fatal exception when checking version at "
496 + buildPropertiesUrl + ":");
497 System.out.println(ex);
498 remoteVersion = getProperty("VERSION");
500 System.setProperty("sun.net.client.defaultConnectTimeout",
503 setProperty("LATEST_VERSION", remoteVersion);
507 VersionChecker vc = new VersionChecker();
512 if (jnlpVersion != null)
514 setProperty("LATEST_VERSION", jnlpVersion);
518 applicationProperties.remove("LATEST_VERSION");
522 // LOAD USERDEFINED COLOURS
524 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
525 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
529 public static void loadBuildProperties(boolean reportVersion)
531 String codeInstallation = getProperty("INSTALLATION");
532 boolean printV = codeInstallation == null;
534 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
537 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
538 .getCodeSource().getLocation().toString()
539 .concat("!/.build_properties"));
541 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
543 InputStream in = localJarFileURL.openStream();
544 applicationProperties.load(in);
546 } catch (Exception ex)
548 System.out.println("Error reading build details: " + ex);
549 applicationProperties.remove("VERSION");
551 String codeVersion = getProperty("VERSION");
552 codeInstallation = getProperty("INSTALLATION");
554 if (codeVersion == null)
556 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
557 codeVersion = "Test";
558 codeInstallation = "";
562 codeInstallation = " (" + codeInstallation + ")";
564 setProperty("VERSION", codeVersion);
565 new BuildDetails(codeVersion, null, codeInstallation);
566 if (printV && reportVersion)
569 "Jalview Version: " + codeVersion + codeInstallation);
573 private static void deleteBuildProperties()
575 applicationProperties.remove("LATEST_VERSION");
576 applicationProperties.remove("VERSION");
577 applicationProperties.remove("AUTHORS");
578 applicationProperties.remove("AUTHORFNAMES");
579 applicationProperties.remove("YEAR");
580 applicationProperties.remove("BUILD_DATE");
581 applicationProperties.remove("INSTALLATION");
585 * Gets Jalview application property of given key. Returns null if key not
591 * @return Property value
593 public static String getProperty(String key)
595 return applicationProperties.getProperty(key);
599 * These methods are used when checking if the saved preference is different
600 * to the default setting
603 public static boolean getDefault(String property, boolean def)
605 String string = getProperty(property);
608 def = Boolean.valueOf(string).booleanValue();
614 public static int getDefault(String property, int def)
616 String string = getProperty(property);
621 def = Integer.parseInt(string);
622 } catch (NumberFormatException e)
624 System.out.println("Error parsing int property '" + property
625 + "' with value '" + string + "'");
633 * These methods are used when checking if the saved preference is different
634 * to the default setting
636 public static String getDefault(String property, String def)
638 String string = getProperty(property);
648 * Stores property in the file "HOME_DIR/.jalview_properties"
653 * String value of property
655 * @return previous value of property (or null)
657 public static Object setProperty(String key, String obj)
659 Object oldValue = null;
662 oldValue = applicationProperties.setProperty(key, obj);
663 if (propertiesFile != null && !propsAreReadOnly)
665 FileOutputStream out = new FileOutputStream(propertiesFile);
666 applicationProperties.store(out, "---JalviewX Properties File---");
669 } catch (Exception ex)
672 "Error setting property: " + key + " " + obj + "\n" + ex);
678 * remove the specified property from the jalview properties file
682 public static void removeProperty(String string)
684 applicationProperties.remove(string);
689 * save the properties to the jalview properties path
691 public static void saveProperties()
693 if (!propsAreReadOnly)
697 FileOutputStream out = new FileOutputStream(propertiesFile);
698 applicationProperties.store(out, "---JalviewX Properties File---");
700 } catch (Exception ex)
702 System.out.println("Error saving properties: " + ex);
708 * internal vamsas class discovery state
710 private static int vamsasJarsArePresent = -1;
713 * Searches for vamsas client classes on class path.
715 * @return true if vamsas client is present on classpath
717 public static boolean vamsasJarsPresent()
719 if (vamsasJarsArePresent == -1)
723 if (jalview.jbgui.GDesktop.class.getClassLoader()
724 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
726 jalview.bin.Cache.log.debug(
727 "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
728 vamsasJarsArePresent = 1;
729 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
730 lvclient.setLevel(Level.toLevel(Cache
731 .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
733 lvclient.addAppender(log.getAppender("JalviewLogger"));
734 // Tell the user that debug is enabled
735 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
737 } catch (Exception e)
739 vamsasJarsArePresent = 0;
740 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
743 return (vamsasJarsArePresent > 0);
747 * internal vamsas class discovery state
749 private static int groovyJarsArePresent = -1;
752 * Searches for vamsas client classes on class path.
754 * @return true if vamsas client is present on classpath
756 public static boolean groovyJarsPresent()
758 if (groovyJarsArePresent == -1)
762 if (Cache.class.getClassLoader()
763 .loadClass("groovy.lang.GroovyObject") != null)
765 jalview.bin.Cache.log.debug(
766 "Found Groovy (groovy.lang.GroovyObject can be loaded)");
767 groovyJarsArePresent = 1;
768 Logger lgclient = Logger.getLogger("groovy");
769 lgclient.setLevel(Level.toLevel(Cache
770 .getDefault("logs.Groovy.Level", Level.INFO.toString())));
772 lgclient.addAppender(log.getAppender("JalviewLogger"));
773 // Tell the user that debug is enabled
774 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
778 groovyJarsArePresent = 0;
779 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
780 } catch (Exception e)
782 groovyJarsArePresent = 0;
783 jalview.bin.Cache.log.debug("Groovy Classes are not present");
786 return (groovyJarsArePresent > 0);
790 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
793 protected static Object tracker = null;
795 protected static Class trackerfocus = null;
797 protected static Class jgoogleanalyticstracker = null;
800 * Initialise the google tracker if it is not done already.
802 public static void initGoogleTracker()
806 if (jgoogleanalyticstracker == null)
808 // try to get the tracker class
811 jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
812 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
813 trackerfocus = Cache.class.getClassLoader()
814 .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
815 } catch (Exception e)
818 "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
820 jgoogleanalyticstracker = null;
825 // now initialise tracker
826 Exception re = null, ex = null;
828 String vrs = "No Version Accessible";
831 // Google analytics tracking code for Library Finder
832 tracker = jgoogleanalyticstracker
833 .getConstructor(new Class[]
834 { String.class, String.class, String.class })
835 .newInstance(new Object[]
837 (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
838 + jalview.bin.Cache.getDefault("BUILD_DATE",
841 jgoogleanalyticstracker
842 .getMethod("trackAsynchronously", new Class[]
844 .invoke(tracker, new Object[]
845 { trackerfocus.getConstructor(new Class[] { String.class })
846 .newInstance(new Object[]
847 { "Application Started." }) });
848 } catch (RuntimeException e)
851 } catch (Exception e)
858 if (re != null || ex != null || err != null)
864 log.debug("Caught runtime exception in googletracker init:",
870 "Failed to initialise GoogleTracker for Jalview Desktop with version "
877 "Whilst initing GoogleTracker for Jalview Desktop version "
887 "Debug: Caught runtime exception in googletracker init:"
889 re.printStackTrace();
894 "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
896 ex.printStackTrace();
902 "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
904 err.printStackTrace();
910 log.debug("Successfully initialised tracker.");
916 * get the user's default colour if available
922 public static Color getDefaultColour(String property, Color defcolour)
924 String colprop = getProperty(property);
929 Color col = ColorUtils.parseColourString(colprop);
932 log.warn("Couldn't parse '" + colprop + "' as a colour for "
935 return (col == null) ? defcolour : col;
939 * store a colour as a Jalview user default property
944 public static void setColourProperty(String property, Color colour)
946 setProperty(property, jalview.util.Format.getHexString(colour));
950 * Stores a formatted date in a jalview property, using a fixed locale.
952 * @param propertyName
954 * @return the formatted date string
956 public static String setDateProperty(String propertyName, Date date)
958 String formatted = date_format.format(date);
959 setProperty(propertyName, formatted);
964 * Reads a date stored in a Jalview property, parses it (using a fixed locale
965 * format) and returns as a Date, or null if parsing fails
967 * @param propertyName
971 public static Date getDateProperty(String propertyName)
973 String val = getProperty(propertyName);
978 return date_format.parse(val);
979 } catch (Exception ex)
981 System.err.println("Invalid or corrupt date in property '"
982 + propertyName + "' : value was '" + val + "'");
989 * get and parse a property as an integer. send any parsing problems to
993 * @return null or Integer
995 public static Integer getIntegerProperty(String property)
997 String val = getProperty(property);
998 if (val != null && (val = val.trim()).length() > 0)
1002 return Integer.valueOf(val);
1003 } catch (NumberFormatException x)
1005 System.err.println("Invalid integer in property '" + property
1006 + "' (value was '" + val + "')");
1013 * Set the specified value, or remove it if null or empty. Does not save the
1019 public static void setOrRemove(String propName, String value)
1021 if (propName == null)
1025 if (value == null || value.trim().length() < 1)
1027 Cache.applicationProperties.remove(propName);
1031 Cache.applicationProperties.setProperty(propName, value);
1036 * Loads in user colour schemes from files.
1039 * a '|'-delimited list of file paths
1041 public static void initUserColourSchemes(String files)
1043 if (files == null || files.length() == 0)
1048 // In case colours can't be loaded, we'll remove them
1049 // from the default list here.
1050 StringBuffer coloursFound = new StringBuffer();
1051 StringTokenizer st = new StringTokenizer(files, "|");
1052 while (st.hasMoreElements())
1054 String file = st.nextToken();
1057 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1060 if (coloursFound.length() > 0)
1062 coloursFound.append("|");
1064 coloursFound.append(file);
1065 ColourSchemes.getInstance().registerColourScheme(ucs);
1067 } catch (Exception ex)
1069 System.out.println("Error loading User ColourFile\n" + ex);
1072 if (!files.equals(coloursFound.toString()))
1074 if (coloursFound.toString().length() > 1)
1076 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1077 coloursFound.toString());
1081 applicationProperties
1082 .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1088 * Initial logging information helper for various versions output
1092 * @param defaultValue
1094 private static void appendIfNotNull(StringBuilder sb, String prefix,
1095 String value, String suffix, String defaultValue)
1097 if (value == null && defaultValue == null)
1101 String line = prefix + (value != null ? value : defaultValue) + suffix;
1107 * @return Jalview version, build details and JVM platform version for console
1109 public static String getVersionDetailsForConsole()
1111 StringBuilder sb = new StringBuilder();
1112 sb.append("Jalview Version: ");
1113 sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
1115 sb.append("Jalview Installation: ");
1116 sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
1118 sb.append("Build Date: ");
1119 sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
1121 sb.append("Java version: ");
1122 sb.append(System.getProperty("java.version"));
1124 sb.append(System.getProperty("os.arch"));
1126 sb.append(System.getProperty("os.name"));
1128 sb.append(System.getProperty("os.version"));
1130 appendIfNotNull(sb, "Install4j version: ",
1131 System.getProperty("sys.install4jVersion"), "\n", null);
1132 appendIfNotNull(sb, "Install4j template version: ",
1133 System.getProperty("installer_template_version"), "\n", null);
1134 appendIfNotNull(sb, "Launcher version: ",
1135 System.getProperty("launcher_version"), "\n", null);
1136 LookAndFeel laf = UIManager.getLookAndFeel();
1137 String lafName = laf == null ? "Not obtained" : laf.getName();
1138 String lafClass = laf == null ? "unknown" : laf.getClass().getName();
1139 sb.append("LookAndFeel: ");
1142 sb.append(lafClass);
1144 // Not displayed in release version ( determined by possible version number
1145 // regex 9[9.]*9[.-_a9]* )
1146 if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
1147 jalview.bin.Cache.getDefault("VERSION", "TEST")))
1149 appendIfNotNull(sb, "Getdown appdir: ",
1150 System.getProperty("getdownappdir"), "\n", null);
1151 appendIfNotNull(sb, "Getdown appbase: ",
1152 System.getProperty("getdownappbase"), "\n", null);
1153 appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
1156 return sb.toString();
1161 * @return build details as reported in splashscreen
1163 public static String getBuildDetailsForSplash()
1165 // consider returning more human friendly info
1166 // eg 'built from Source' or update channel
1167 return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
1170 public static String getStackTraceString(Throwable t)
1172 StringWriter sw = new StringWriter();
1173 PrintWriter pw = new PrintWriter(sw);
1174 t.printStackTrace(pw);
1175 return sw.toString();
1179 * Getdown appbase methods
1182 private static final String releaseAppbase;
1184 private static String getdownAppbase;
1186 private static String getdownDistDir;
1190 Float specversion = Float
1191 .parseFloat(System.getProperty("java.specification.version"));
1192 releaseAppbase = (specversion < 9)
1193 ? "https://www.jalview.org/getdown/release/1.8"
1194 : "https://www.jalview.org/getdown/release/11";
1197 // look for properties (passed in by getdown) otherwise default to release
1198 private static void setGetdownAppbase()
1200 if (getdownAppbase != null)
1204 String appbase = System.getProperty("getdownappbase");
1205 String distDir = System.getProperty("getdowndistdir");
1206 if (appbase == null)
1208 appbase = releaseAppbase;
1209 distDir = "release";
1211 if (appbase.endsWith("/"))
1213 appbase = appbase.substring(0, appbase.length() - 1);
1215 if (distDir == null)
1217 distDir = appbase.equals(releaseAppbase) ? "release" : "alt";
1219 getdownAppbase = appbase;
1220 getdownDistDir = distDir;
1223 public static String getGetdownAppbase()
1225 setGetdownAppbase();
1226 return getdownAppbase;
1229 public static String getAppbaseBuildProperties()
1231 String appbase = getGetdownAppbase();
1232 return appbase + "/" + getdownDistDir + "/build_properties";