2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.datamodel.PDBEntry;
24 import jalview.gui.UserDefinedColours;
25 import jalview.schemes.ColourSchemeLoader;
26 import jalview.schemes.ColourSchemes;
27 import jalview.schemes.UserColourScheme;
28 import jalview.structure.StructureImportSettings;
29 import jalview.urls.IdOrgSettings;
30 import jalview.util.ColorUtils;
31 import jalview.util.Platform;
32 import jalview.ws.sifts.SiftsSettings;
34 import java.awt.Color;
35 import java.io.BufferedReader;
37 import java.io.FileInputStream;
38 import java.io.FileOutputStream;
39 import java.io.InputStream;
40 import java.io.InputStreamReader;
42 import java.text.DateFormat;
43 import java.text.SimpleDateFormat;
44 import java.util.Collections;
45 import java.util.Date;
46 import java.util.Enumeration;
47 import java.util.Locale;
48 import java.util.Properties;
49 import java.util.StringTokenizer;
50 import java.util.TreeSet;
51 import java.util.regex.Pattern;
53 import javax.swing.LookAndFeel;
54 import javax.swing.UIManager;
56 import org.apache.log4j.ConsoleAppender;
57 import org.apache.log4j.Level;
58 import org.apache.log4j.Logger;
59 import org.apache.log4j.SimpleLayout;
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 = Platform.isJS();
288 private final static String JS_PROPERTY_PREFIX = "jalview_";
290 public static void initLogger()
298 // TODO: redirect stdout and stderr here in order to grab the output of
301 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
303 ap.setName("JalviewLogger");
304 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
306 Logger laxis = Logger.getLogger("org.apache.axis");
307 Logger lcastor = Logger.getLogger("org.exolab.castor");
308 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
310 laxis.setLevel(Level.toLevel(
311 Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
312 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
313 Level.INFO.toString())));
314 lcastor = Logger.getLogger("org.exolab.castor.xml");
315 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
316 Level.INFO.toString())));
317 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
318 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
319 // Level.INFO.toString())));
320 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
321 .getDefault("logs.Jalview.level", Level.INFO.toString())));
322 // laxis.addAppender(ap);
323 // lcastor.addAppender(ap);
324 // jalview.bin.Cache.log.addAppender(ap);
325 // Tell the user that debug is enabled
326 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
327 } catch (Exception ex)
329 System.err.println("Problems initializing the log4j system\n");
330 ex.printStackTrace(System.err);
335 * Loads properties from the given properties file. Any existing properties
338 public static void loadProperties(String propsFile)
340 propertiesFile = propsFile;
341 if (propsFile == null && !propsAreReadOnly)
343 propertiesFile = System.getProperty("user.home") + File.separatorChar
344 + ".jalview_properties";
348 // don't corrupt the file we've been given.
349 propsAreReadOnly = true;
352 if (propertiesFile == null)
354 Platform.readInfoProperties(JS_PROPERTY_PREFIX,
355 applicationProperties);
364 fis = new java.net.URL(propertiesFile).openStream();
366 "Loading jalview properties from : " + propertiesFile);
368 "Disabling Jalview writing to user's local properties file.");
369 propsAreReadOnly = true;
371 } catch (Exception ex)
377 fis = new FileInputStream(propertiesFile);
379 applicationProperties.clear();
380 applicationProperties.load(fis);
382 // remove any old build properties
384 deleteBuildProperties();
386 } catch (Exception ex)
388 System.out.println("Error reading properties file: " + ex);
391 if (getDefault("USE_PROXY", false))
393 String proxyServer = getDefault("PROXY_SERVER", ""),
394 proxyPort = getDefault("PROXY_PORT", "8080");
396 System.out.println("Using proxyServer: " + proxyServer
397 + " proxyPort: " + proxyPort);
399 System.setProperty("http.proxyHost", proxyServer);
400 System.setProperty("http.proxyPort", proxyPort);
403 // LOAD THE AUTHORS FROM THE authors.props file
404 String authorDetails = resolveResourceURLFor("/authors.props");
408 if (authorDetails != null)
410 URL localJarFileURL = new URL(authorDetails);
411 InputStream in = localJarFileURL.openStream();
412 applicationProperties.load(in);
415 } catch (Exception ex)
417 System.out.println("Error reading author details: " + ex);
418 authorDetails = null;
420 if (authorDetails == null)
422 applicationProperties.remove("AUTHORS");
423 applicationProperties.remove("AUTHORFNAMES");
424 applicationProperties.remove("YEAR");
427 loadBuildProperties(false);
430 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
432 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
433 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
435 SiftsSettings.setFailSafePIDThreshold(
436 jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
437 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
439 SiftsSettings.setCacheThresholdInDays(
440 jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
441 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
443 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
444 "http://www.jalview.org/services/identifiers"));
445 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
447 StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
448 .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
449 StructureImportSettings
450 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
451 // StructureImportSettings
452 // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
453 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
455 String jnlpVersion = System.getProperty("jalview.version");
457 // jnlpVersion will be null if a latest version check for the channel needs to
459 // Dont do this check if running in headless mode
461 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
462 && (System.getProperty("java.awt.headless") == null || System
463 .getProperty("java.awt.headless").equals("false")))
470 String orgtimeout = System
471 .getProperty("sun.net.client.defaultConnectTimeout");
472 if (orgtimeout == null)
475 System.out.println("# INFO: Setting default net timeout to "
476 + orgtimeout + " seconds.");
478 String remoteVersion = null;
481 System.setProperty("sun.net.client.defaultConnectTimeout",
483 java.net.URL url = new java.net.URL(Cache
484 .getDefault("www.jalview.org", "http://www.jalview.org")
485 + "/webstart/jalview.jnlp");
486 BufferedReader in = new BufferedReader(
487 new InputStreamReader(url.openStream()));
489 while ((line = in.readLine()) != null)
491 if (line.indexOf("jalview.version") == -1)
496 line = line.substring(line.indexOf("value=") + 7);
497 line = line.substring(0, line.lastIndexOf("\""));
498 remoteVersion = line;
501 } catch (Exception ex)
504 "Non-fatal exception when checking version at www.jalview.org :");
505 System.out.println(ex);
506 remoteVersion = getProperty("VERSION");
508 System.setProperty("sun.net.client.defaultConnectTimeout",
511 setProperty("LATEST_VERSION", remoteVersion);
517 if (jnlpVersion != null)
519 setProperty("LATEST_VERSION", jnlpVersion);
523 applicationProperties.remove("LATEST_VERSION");
527 // LOAD USERDEFINED COLOURS
528 Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
529 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
534 * construct a resource URL for the given absolute resource pathname
536 * @param resourcePath
539 private static String resolveResourceURLFor(String resourcePath)
542 if (Platform.isJS() || !Cache.class.getProtectionDomain()
543 .getCodeSource().getLocation().toString().endsWith(".jar"))
547 url = Cache.class.getResource(resourcePath).toString();
548 } catch (Exception ex)
550 System.err.println("Failed to resolve resource " + resourcePath + ": "
556 url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
557 .getLocation().toString().concat("!" + resourcePath));
562 public static void loadBuildProperties(boolean reportVersion)
564 String codeInstallation = getProperty("INSTALLATION");
565 boolean printVersion = codeInstallation == null;
568 * read build properties - from the Jalview jar for a Java distribution,
569 * or from codebase file in test or JalviewJS context
573 String buildDetails = resolveResourceURLFor("/.build_properties");
574 URL localJarFileURL = new URL(buildDetails);
575 InputStream in = localJarFileURL.openStream();
576 applicationProperties.load(in);
578 } catch (Exception ex)
580 System.out.println("Error reading build details: " + ex);
581 applicationProperties.remove("VERSION");
583 String codeVersion = getProperty("VERSION");
584 codeInstallation = getProperty("INSTALLATION");
586 if (codeVersion == null)
588 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
589 codeVersion = "Test";
590 codeInstallation = "";
594 codeInstallation = " (" + codeInstallation + ")";
596 setProperty("VERSION", codeVersion);
597 new BuildDetails(codeVersion, null, codeInstallation);
598 if (printVersion && reportVersion)
601 .println("Jalview Version: " + codeVersion + codeInstallation);
605 private static void deleteBuildProperties()
607 applicationProperties.remove("LATEST_VERSION");
608 applicationProperties.remove("VERSION");
609 applicationProperties.remove("AUTHORS");
610 applicationProperties.remove("AUTHORFNAMES");
611 applicationProperties.remove("YEAR");
612 applicationProperties.remove("BUILD_DATE");
613 applicationProperties.remove("INSTALLATION");
617 * Gets Jalview application property of given key. Returns null if key not
623 * @return Property value
625 public static String getProperty(String key)
627 String prop = applicationProperties.getProperty(key);
628 if (prop == null && Platform.isJS())
630 prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
631 + "_" + JS_PROPERTY_PREFIX + key);
637 * These methods are used when checking if the saved preference is different
638 * to the default setting
641 public static boolean getDefault(String property, boolean def)
643 String string = getProperty(property);
646 def = Boolean.valueOf(string).booleanValue();
652 public static int getDefault(String property, int def)
654 String string = getProperty(property);
659 def = Integer.parseInt(string);
660 } catch (NumberFormatException e)
662 System.out.println("Error parsing int property '" + property
663 + "' with value '" + string + "'");
671 * Answers the value of the given property, or the supplied default value if
672 * the property is not set
674 public static String getDefault(String property, String def)
676 String value = getProperty(property);
677 return value == null ? def : value;
681 * Stores property in the file "HOME_DIR/.jalview_properties"
686 * String value of property
688 * @return previous value of property (or null)
690 public static Object setProperty(String key, String obj)
692 Object oldValue = null;
695 oldValue = applicationProperties.setProperty(key, obj);
696 if (propertiesFile != null && !propsAreReadOnly)
698 FileOutputStream out = new FileOutputStream(propertiesFile);
699 applicationProperties.store(out, "---JalviewX Properties File---");
702 } catch (Exception ex)
705 "Error setting property: " + key + " " + obj + "\n" + ex);
711 * remove the specified property from the jalview properties file
715 public static void removeProperty(String string)
717 applicationProperties.remove(string);
722 * save the properties to the jalview properties path
724 public static void saveProperties()
726 if (!propsAreReadOnly)
730 FileOutputStream out = new FileOutputStream(propertiesFile);
731 applicationProperties.store(out, "---JalviewX Properties File---");
733 } catch (Exception ex)
735 System.out.println("Error saving properties: " + ex);
741 * internal vamsas class discovery state
743 private static int vamsasJarsArePresent = -1;
746 * Searches for vamsas client classes on class path.
748 * @return true if vamsas client is present on classpath
750 public static boolean vamsasJarsPresent()
752 if (vamsasJarsArePresent == -1)
756 if (jalview.jbgui.GDesktop.class.getClassLoader()
757 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
759 jalview.bin.Cache.log.debug(
760 "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
761 vamsasJarsArePresent = 1;
762 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
763 lvclient.setLevel(Level.toLevel(Cache
764 .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
766 lvclient.addAppender(log.getAppender("JalviewLogger"));
767 // Tell the user that debug is enabled
768 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
770 } catch (Exception e)
772 vamsasJarsArePresent = 0;
773 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
776 return (vamsasJarsArePresent > 0);
780 * internal vamsas class discovery state
782 private static int groovyJarsArePresent = -1;
785 * Searches for vamsas client classes on class path.
787 * @return true if vamsas client is present on classpath
789 public static boolean groovyJarsPresent()
791 if (groovyJarsArePresent == -1)
795 if (Cache.class.getClassLoader()
796 .loadClass("groovy.lang.GroovyObject") != null)
798 jalview.bin.Cache.log.debug(
799 "Found Groovy (groovy.lang.GroovyObject can be loaded)");
800 groovyJarsArePresent = 1;
801 Logger lgclient = Logger.getLogger("groovy");
802 lgclient.setLevel(Level.toLevel(Cache
803 .getDefault("logs.Groovy.Level", Level.INFO.toString())));
805 lgclient.addAppender(log.getAppender("JalviewLogger"));
806 // Tell the user that debug is enabled
807 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
811 groovyJarsArePresent = 0;
812 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
813 } catch (Exception e)
815 groovyJarsArePresent = 0;
816 jalview.bin.Cache.log.debug("Groovy Classes are not present");
819 return (groovyJarsArePresent > 0);
823 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
826 protected static Object tracker = null;
828 protected static Class trackerfocus = null;
830 protected static Class jgoogleanalyticstracker = null;
833 * Initialise the google tracker if it is not done already.
835 public static void initGoogleTracker()
839 if (jgoogleanalyticstracker == null)
841 // try to get the tracker class
844 jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
845 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
846 trackerfocus = Cache.class.getClassLoader()
847 .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
848 } catch (Exception e)
851 "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
853 jgoogleanalyticstracker = null;
858 // now initialise tracker
859 Exception re = null, ex = null;
861 String vrs = "No Version Accessible";
864 // Google analytics tracking code for Library Finder
865 tracker = jgoogleanalyticstracker
866 .getConstructor(new Class[]
867 { String.class, String.class, String.class })
868 .newInstance(new Object[]
870 (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
871 + jalview.bin.Cache.getDefault("BUILD_DATE",
874 jgoogleanalyticstracker
875 .getMethod("trackAsynchronously", new Class[]
877 .invoke(tracker, new Object[]
878 { trackerfocus.getConstructor(new Class[] { String.class })
879 .newInstance(new Object[]
880 { "Application Started." }) });
881 } catch (RuntimeException e)
884 } catch (Exception e)
891 if (re != null || ex != null || err != null)
897 log.debug("Caught runtime exception in googletracker init:",
903 "Failed to initialise GoogleTracker for Jalview Desktop with version "
910 "Whilst initing GoogleTracker for Jalview Desktop version "
920 "Debug: Caught runtime exception in googletracker init:"
922 re.printStackTrace();
927 "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
929 ex.printStackTrace();
935 "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
937 err.printStackTrace();
943 log.debug("Successfully initialised tracker.");
949 * get the user's default colour if available
955 public static Color getDefaultColour(String property, Color defcolour)
957 String colprop = getProperty(property);
962 Color col = ColorUtils.parseColourString(colprop);
965 log.warn("Couldn't parse '" + colprop + "' as a colour for "
968 return (col == null) ? defcolour : col;
972 * store a colour as a Jalview user default property
977 public static void setColourProperty(String property, Color colour)
979 setProperty(property, jalview.util.Format.getHexString(colour));
983 * Stores a formatted date in a jalview property, using a fixed locale.
985 * @param propertyName
987 * @return the formatted date string
989 public static String setDateProperty(String propertyName, Date date)
991 String formatted = date_format.format(date);
992 setProperty(propertyName, formatted);
997 * Reads a date stored in a Jalview property, parses it (using a fixed locale
998 * format) and returns as a Date, or null if parsing fails
1000 * @param propertyName
1004 public static Date getDateProperty(String propertyName)
1006 String val = getProperty(propertyName);
1011 return date_format.parse(val);
1012 } catch (Exception ex)
1014 System.err.println("Invalid or corrupt date in property '"
1015 + propertyName + "' : value was '" + val + "'");
1022 * get and parse a property as an integer. send any parsing problems to
1026 * @return null or Integer
1028 public static Integer getIntegerProperty(String property)
1030 String val = getProperty(property);
1031 if (val != null && (val = val.trim()).length() > 0)
1035 return Integer.valueOf(val);
1036 } catch (NumberFormatException x)
1038 System.err.println("Invalid integer in property '" + property
1039 + "' (value was '" + val + "')");
1046 * Set the specified value, or remove it if null or empty. Does not save the
1052 public static void setOrRemove(String propName, String value)
1054 if (propName == null)
1058 if (value == null || value.trim().length() < 1)
1060 Cache.applicationProperties.remove(propName);
1064 Cache.applicationProperties.setProperty(propName, value);
1069 * Loads in user colour schemes from files.
1072 * a '|'-delimited list of file paths
1074 public static void initUserColourSchemes(String files)
1076 if (files == null || files.length() == 0)
1081 // In case colours can't be loaded, we'll remove them
1082 // from the default list here.
1083 StringBuffer coloursFound = new StringBuffer();
1084 StringTokenizer st = new StringTokenizer(files, "|");
1085 while (st.hasMoreElements())
1087 String file = st.nextToken();
1090 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1093 if (coloursFound.length() > 0)
1095 coloursFound.append("|");
1097 coloursFound.append(file);
1098 ColourSchemes.getInstance().registerColourScheme(ucs);
1100 } catch (Exception ex)
1102 System.out.println("Error loading User ColourFile\n" + ex);
1105 if (!files.equals(coloursFound.toString()))
1107 if (coloursFound.toString().length() > 1)
1109 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1110 coloursFound.toString());
1114 applicationProperties
1115 .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1121 * Initial logging information helper for various versions output
1125 * @param defaultValue
1127 private static void appendIfNotNull(StringBuilder sb, String prefix,
1128 String value, String suffix, String defaultValue)
1130 if (value == null && defaultValue == null)
1134 String line = prefix + (value != null ? value : defaultValue) + suffix;
1140 * @return Jalview version, build details and JVM platform version for console
1142 public static String getVersionDetailsForConsole()
1144 StringBuilder sb = new StringBuilder();
1145 sb.append("Jalview Version: " + jalview.bin.Cache.getDefault("VERSION", "TEST"));
1147 sb.append("Jalview Installation: "
1148 + jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
1150 sb.append("Build Date: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
1152 sb.append("Java version: " + System.getProperty("java.version"));
1154 sb.append(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version"));
1156 appendIfNotNull(sb, "Install4j version: ",
1157 System.getProperty("sys.install4jVersion"), "\n", null);
1158 appendIfNotNull(sb, "Install4j template version: ",
1159 System.getProperty("installer_template_version"), "\n", null);
1160 appendIfNotNull(sb, "Launcher version: ",
1161 System.getProperty("launcher_version"), "\n", null);
1162 LookAndFeel laf = UIManager.getLookAndFeel();
1163 String lafName = laf == null?"Not obtained":laf.getName();
1164 String lafClass = laf == null?"unknown":laf.getClass().getName();
1165 appendIfNotNull(sb, "LookAndFeel: ", lafName+" ("+lafClass+")", "\n", null);
1166 // Not displayed in release version ( determined by possible version number regex 9[9.]*9[.-_a9]* )
1167 if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$", jalview.bin.Cache.getDefault("VERSION", "TEST"))) {
1168 appendIfNotNull(sb, "Getdown appdir: ",
1169 System.getProperty("getdownappdir"), "\n", null);
1170 appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
1173 return sb.toString();
1178 * @return build details as reported in splashscreen
1180 public static String getBuildDetailsForSplash()
1182 // consider returning more human friendly info
1183 // eg 'built from Source' or update channel
1184 return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");