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 (http://www.jalview.org) a property enabling all HTTP
178 * requests to be redirected to a mirror of http://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 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
319 .getDefault("logs.Jalview.level", Level.INFO.toString())));
320 // laxis.addAppender(ap);
321 // lcastor.addAppender(ap);
322 // jalview.bin.Cache.log.addAppender(ap);
323 // Tell the user that debug is enabled
324 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
325 } catch (Exception ex)
327 System.err.println("Problems initializing the log4j system\n");
328 ex.printStackTrace(System.err);
333 * Loads properties from the given properties file. Any existing properties
336 public static void loadProperties(String propsFile)
338 propertiesFile = propsFile;
339 if (propsFile == null)
341 propertiesFile = System.getProperty("user.home") + File.separatorChar
342 + ".jalview_properties";
346 // don't corrupt the file we've been given.
347 propsAreReadOnly = true;
355 fis = new java.net.URL(propertiesFile).openStream();
357 "Loading jalview properties from : " + propertiesFile);
359 "Disabling Jalview writing to user's local properties file.");
360 propsAreReadOnly = true;
362 } catch (Exception ex)
368 fis = new FileInputStream(propertiesFile);
370 applicationProperties.clear();
371 applicationProperties.load(fis);
373 // remove any old build properties
375 deleteBuildProperties();
377 } catch (Exception ex)
379 System.out.println("Error reading properties file: " + ex);
382 if (getDefault("USE_PROXY", false))
384 String proxyServer = getDefault("PROXY_SERVER", ""),
385 proxyPort = getDefault("PROXY_PORT", "8080");
387 System.out.println("Using proxyServer: " + proxyServer
388 + " proxyPort: " + proxyPort);
390 System.setProperty("http.proxyHost", proxyServer);
391 System.setProperty("http.proxyPort", proxyPort);
394 // LOAD THE AUTHORS FROM THE authors.props file
397 String authorDetails = "jar:"
398 .concat(Cache.class.getProtectionDomain().getCodeSource()
399 .getLocation().toString().concat("!/authors.props"));
401 java.net.URL localJarFileURL = new java.net.URL(authorDetails);
403 InputStream in = localJarFileURL.openStream();
404 applicationProperties.load(in);
406 } catch (Exception ex)
408 System.out.println("Error reading author details: " + ex);
409 applicationProperties.remove("AUTHORS");
410 applicationProperties.remove("AUTHORFNAMES");
411 applicationProperties.remove("YEAR");
414 loadBuildProperties(false);
417 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
419 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
420 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
422 SiftsSettings.setFailSafePIDThreshold(
423 jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
424 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
426 SiftsSettings.setCacheThresholdInDays(
427 jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
428 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
430 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
431 "http://www.jalview.org/services/identifiers"));
432 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
434 StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
435 .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
436 StructureImportSettings
437 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
438 // StructureImportSettings
439 // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
440 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
442 String jnlpVersion = System.getProperty("jalview.version");
444 // jnlpVersion will be null if a latest version check for the channel needs
446 // Dont do this check if running in headless mode
448 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
449 && (System.getProperty("java.awt.headless") == null || System
450 .getProperty("java.awt.headless").equals("false")))
453 class VersionChecker extends Thread
458 String orgtimeout = System
459 .getProperty("sun.net.client.defaultConnectTimeout");
460 if (orgtimeout == null)
463 System.out.println("# INFO: Setting default net timeout to "
464 + orgtimeout + " seconds.");
466 String remoteVersion = null;
469 System.setProperty("sun.net.client.defaultConnectTimeout",
471 java.net.URL url = new java.net.URL(Cache
472 .getDefault("www.jalview.org", "http://www.jalview.org")
473 + "/webstart/jalview.jnlp");
474 BufferedReader in = new BufferedReader(
475 new InputStreamReader(url.openStream()));
477 while ((line = in.readLine()) != null)
479 if (line.indexOf("jalview.version") == -1)
484 line = line.substring(line.indexOf("value=") + 7);
485 line = line.substring(0, line.lastIndexOf("\""));
486 remoteVersion = line;
489 } catch (Exception ex)
492 "Non-fatal exception when checking version at www.jalview.org :");
493 System.out.println(ex);
494 remoteVersion = getProperty("VERSION");
496 System.setProperty("sun.net.client.defaultConnectTimeout",
499 setProperty("LATEST_VERSION", remoteVersion);
503 VersionChecker vc = new VersionChecker();
508 if (jnlpVersion != null)
510 setProperty("LATEST_VERSION", jnlpVersion);
514 applicationProperties.remove("LATEST_VERSION");
518 // LOAD USERDEFINED COLOURS
520 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
521 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
525 public static void loadBuildProperties(boolean reportVersion)
527 String codeInstallation = getProperty("INSTALLATION");
528 boolean printV = codeInstallation == null;
530 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
533 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
534 .getCodeSource().getLocation().toString()
535 .concat("!/.build_properties"));
537 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
539 InputStream in = localJarFileURL.openStream();
540 applicationProperties.load(in);
542 } catch (Exception ex)
544 System.out.println("Error reading build details: " + ex);
545 applicationProperties.remove("VERSION");
547 String codeVersion = getProperty("VERSION");
548 codeInstallation = getProperty("INSTALLATION");
550 if (codeVersion == null)
552 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
553 codeVersion = "Test";
554 codeInstallation = "";
558 codeInstallation = " (" + codeInstallation + ")";
560 setProperty("VERSION", codeVersion);
561 new BuildDetails(codeVersion, null, codeInstallation);
562 if (printV && reportVersion)
565 "Jalview Version: " + codeVersion + codeInstallation);
569 private static void deleteBuildProperties()
571 applicationProperties.remove("LATEST_VERSION");
572 applicationProperties.remove("VERSION");
573 applicationProperties.remove("AUTHORS");
574 applicationProperties.remove("AUTHORFNAMES");
575 applicationProperties.remove("YEAR");
576 applicationProperties.remove("BUILD_DATE");
577 applicationProperties.remove("INSTALLATION");
581 * Gets Jalview application property of given key. Returns null if key not
587 * @return Property value
589 public static String getProperty(String key)
591 return applicationProperties.getProperty(key);
595 * These methods are used when checking if the saved preference is different
596 * to the default setting
599 public static boolean getDefault(String property, boolean def)
601 String string = getProperty(property);
604 def = Boolean.valueOf(string).booleanValue();
610 public static int getDefault(String property, int def)
612 String string = getProperty(property);
617 def = Integer.parseInt(string);
618 } catch (NumberFormatException e)
620 System.out.println("Error parsing int property '" + property
621 + "' with value '" + string + "'");
629 * These methods are used when checking if the saved preference is different
630 * to the default setting
632 public static String getDefault(String property, String def)
634 String string = getProperty(property);
644 * Stores property in the file "HOME_DIR/.jalview_properties"
649 * String value of property
651 * @return previous value of property (or null)
653 public static Object setProperty(String key, String obj)
655 Object oldValue = null;
658 oldValue = applicationProperties.setProperty(key, obj);
659 if (propertiesFile != null && !propsAreReadOnly)
661 FileOutputStream out = new FileOutputStream(propertiesFile);
662 applicationProperties.store(out, "---JalviewX Properties File---");
665 } catch (Exception ex)
668 "Error setting property: " + key + " " + obj + "\n" + ex);
674 * remove the specified property from the jalview properties file
678 public static void removeProperty(String string)
680 applicationProperties.remove(string);
685 * save the properties to the jalview properties path
687 public static void saveProperties()
689 if (!propsAreReadOnly)
693 FileOutputStream out = new FileOutputStream(propertiesFile);
694 applicationProperties.store(out, "---JalviewX Properties File---");
696 } catch (Exception ex)
698 System.out.println("Error saving properties: " + ex);
704 * internal vamsas class discovery state
706 private static int vamsasJarsArePresent = -1;
709 * Searches for vamsas client classes on class path.
711 * @return true if vamsas client is present on classpath
713 public static boolean vamsasJarsPresent()
715 if (vamsasJarsArePresent == -1)
719 if (jalview.jbgui.GDesktop.class.getClassLoader()
720 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
722 jalview.bin.Cache.log.debug(
723 "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
724 vamsasJarsArePresent = 1;
725 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
726 lvclient.setLevel(Level.toLevel(Cache
727 .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
729 lvclient.addAppender(log.getAppender("JalviewLogger"));
730 // Tell the user that debug is enabled
731 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
733 } catch (Exception e)
735 vamsasJarsArePresent = 0;
736 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
739 return (vamsasJarsArePresent > 0);
743 * internal vamsas class discovery state
745 private static int groovyJarsArePresent = -1;
748 * Searches for vamsas client classes on class path.
750 * @return true if vamsas client is present on classpath
752 public static boolean groovyJarsPresent()
754 if (groovyJarsArePresent == -1)
758 if (Cache.class.getClassLoader()
759 .loadClass("groovy.lang.GroovyObject") != null)
761 jalview.bin.Cache.log.debug(
762 "Found Groovy (groovy.lang.GroovyObject can be loaded)");
763 groovyJarsArePresent = 1;
764 Logger lgclient = Logger.getLogger("groovy");
765 lgclient.setLevel(Level.toLevel(Cache
766 .getDefault("logs.Groovy.Level", Level.INFO.toString())));
768 lgclient.addAppender(log.getAppender("JalviewLogger"));
769 // Tell the user that debug is enabled
770 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
774 groovyJarsArePresent = 0;
775 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
776 } catch (Exception e)
778 groovyJarsArePresent = 0;
779 jalview.bin.Cache.log.debug("Groovy Classes are not present");
782 return (groovyJarsArePresent > 0);
786 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
789 protected static Object tracker = null;
791 protected static Class trackerfocus = null;
793 protected static Class jgoogleanalyticstracker = null;
796 * Initialise the google tracker if it is not done already.
798 public static void initGoogleTracker()
802 if (jgoogleanalyticstracker == null)
804 // try to get the tracker class
807 jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
808 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
809 trackerfocus = Cache.class.getClassLoader()
810 .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
811 } catch (Exception e)
814 "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
816 jgoogleanalyticstracker = null;
821 // now initialise tracker
822 Exception re = null, ex = null;
824 String vrs = "No Version Accessible";
827 // Google analytics tracking code for Library Finder
828 tracker = jgoogleanalyticstracker
829 .getConstructor(new Class[]
830 { String.class, String.class, String.class })
831 .newInstance(new Object[]
833 (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
834 + jalview.bin.Cache.getDefault("BUILD_DATE",
837 jgoogleanalyticstracker
838 .getMethod("trackAsynchronously", new Class[]
840 .invoke(tracker, new Object[]
841 { trackerfocus.getConstructor(new Class[] { String.class })
842 .newInstance(new Object[]
843 { "Application Started." }) });
844 } catch (RuntimeException e)
847 } catch (Exception e)
854 if (re != null || ex != null || err != null)
860 log.debug("Caught runtime exception in googletracker init:",
866 "Failed to initialise GoogleTracker for Jalview Desktop with version "
873 "Whilst initing GoogleTracker for Jalview Desktop version "
883 "Debug: Caught runtime exception in googletracker init:"
885 re.printStackTrace();
890 "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
892 ex.printStackTrace();
898 "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
900 err.printStackTrace();
906 log.debug("Successfully initialised tracker.");
912 * get the user's default colour if available
918 public static Color getDefaultColour(String property, Color defcolour)
920 String colprop = getProperty(property);
925 Color col = ColorUtils.parseColourString(colprop);
928 log.warn("Couldn't parse '" + colprop + "' as a colour for "
931 return (col == null) ? defcolour : col;
935 * store a colour as a Jalview user default property
940 public static void setColourProperty(String property, Color colour)
942 setProperty(property, jalview.util.Format.getHexString(colour));
946 * Stores a formatted date in a jalview property, using a fixed locale.
948 * @param propertyName
950 * @return the formatted date string
952 public static String setDateProperty(String propertyName, Date date)
954 String formatted = date_format.format(date);
955 setProperty(propertyName, formatted);
960 * Reads a date stored in a Jalview property, parses it (using a fixed locale
961 * format) and returns as a Date, or null if parsing fails
963 * @param propertyName
967 public static Date getDateProperty(String propertyName)
969 String val = getProperty(propertyName);
974 return date_format.parse(val);
975 } catch (Exception ex)
977 System.err.println("Invalid or corrupt date in property '"
978 + propertyName + "' : value was '" + val + "'");
985 * get and parse a property as an integer. send any parsing problems to
989 * @return null or Integer
991 public static Integer getIntegerProperty(String property)
993 String val = getProperty(property);
994 if (val != null && (val = val.trim()).length() > 0)
998 return Integer.valueOf(val);
999 } catch (NumberFormatException x)
1001 System.err.println("Invalid integer in property '" + property
1002 + "' (value was '" + val + "')");
1009 * Set the specified value, or remove it if null or empty. Does not save the
1015 public static void setOrRemove(String propName, String value)
1017 if (propName == null)
1021 if (value == null || value.trim().length() < 1)
1023 Cache.applicationProperties.remove(propName);
1027 Cache.applicationProperties.setProperty(propName, value);
1032 * Loads in user colour schemes from files.
1035 * a '|'-delimited list of file paths
1037 public static void initUserColourSchemes(String files)
1039 if (files == null || files.length() == 0)
1044 // In case colours can't be loaded, we'll remove them
1045 // from the default list here.
1046 StringBuffer coloursFound = new StringBuffer();
1047 StringTokenizer st = new StringTokenizer(files, "|");
1048 while (st.hasMoreElements())
1050 String file = st.nextToken();
1053 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1056 if (coloursFound.length() > 0)
1058 coloursFound.append("|");
1060 coloursFound.append(file);
1061 ColourSchemes.getInstance().registerColourScheme(ucs);
1063 } catch (Exception ex)
1065 System.out.println("Error loading User ColourFile\n" + ex);
1068 if (!files.equals(coloursFound.toString()))
1070 if (coloursFound.toString().length() > 1)
1072 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1073 coloursFound.toString());
1077 applicationProperties
1078 .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1084 * Initial logging information helper for various versions output
1088 * @param defaultValue
1090 private static void appendIfNotNull(StringBuilder sb, String prefix,
1091 String value, String suffix, String defaultValue)
1093 if (value == null && defaultValue == null)
1097 String line = prefix + (value != null ? value : defaultValue) + suffix;
1103 * @return Jalview version, build details and JVM platform version for console
1105 public static String getVersionDetailsForConsole()
1107 StringBuilder sb = new StringBuilder();
1108 sb.append("Jalview Version: "
1109 + jalview.bin.Cache.getDefault("VERSION", "TEST"));
1111 sb.append("Jalview Installation: "
1112 + jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
1114 sb.append("Build Date: "
1115 + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
1117 sb.append("Java version: " + System.getProperty("java.version"));
1119 sb.append(System.getProperty("os.arch") + " "
1120 + System.getProperty("os.name") + " "
1121 + System.getProperty("os.version"));
1123 appendIfNotNull(sb, "Install4j version: ",
1124 System.getProperty("sys.install4jVersion"), "\n", null);
1125 appendIfNotNull(sb, "Install4j template version: ",
1126 System.getProperty("installer_template_version"), "\n", null);
1127 appendIfNotNull(sb, "Launcher version: ",
1128 System.getProperty("launcher_version"), "\n", null);
1129 LookAndFeel laf = UIManager.getLookAndFeel();
1130 String lafName = laf == null ? "Not obtained" : laf.getName();
1131 String lafClass = laf == null ? "unknown" : laf.getClass().getName();
1132 appendIfNotNull(sb, "LookAndFeel: ", lafName + " (" + lafClass + ")",
1134 // Not displayed in release version ( determined by possible version number
1135 // regex 9[9.]*9[.-_a9]* )
1136 if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
1137 jalview.bin.Cache.getDefault("VERSION", "TEST")))
1139 appendIfNotNull(sb, "Getdown appdir: ",
1140 System.getProperty("getdownappdir"), "\n", null);
1141 appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
1144 return sb.toString();
1149 * @return build details as reported in splashscreen
1151 public static String getBuildDetailsForSplash()
1153 // consider returning more human friendly info
1154 // eg 'built from Source' or update channel
1155 return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
1158 public static String getStackTraceString(Throwable t)
1160 StringWriter sw = new StringWriter();
1161 PrintWriter pw = new PrintWriter(sw);
1162 t.printStackTrace(pw);
1163 return sw.toString();