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;
52 import org.apache.log4j.ConsoleAppender;
53 import org.apache.log4j.Level;
54 import org.apache.log4j.Logger;
55 import org.apache.log4j.SimpleLayout;
58 * Stores and retrieves Jalview Application Properties Lists and fields within
59 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
60 * are alternative values for a tag. <br>
62 * Current properties include:
65 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
66 * logging level for axis (used for web services) <br>
68 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
69 * the logging level for castor (used for serialization) <br>
71 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
73 * <li>SCREEN_WIDTH</li>
74 * <li>SCREEN_HEIGHT</li>
75 * <li>SCREEN_Y=285</li>
76 * <li>SCREEN_X=371</li>
77 * <li>SHOW_FULLSCREEN boolean</li>
78 * <li>FONT_NAME java font name for alignment text display</li>
79 * <li>FONT_SIZE size of displayed alignment text</li>
80 * <li>FONT_STYLE style of font displayed (sequence labels are always
82 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
83 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
84 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
85 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
86 * <li>SHOW_IDENTITY show percentage identity annotation</li>
87 * <li>SHOW_QUALITY show alignment quality annotation</li>
88 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
89 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
90 * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
91 * LABEL_AND_SEQUENCE</li>
92 * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
93 * sequence annotations</li>
94 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
96 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
97 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
98 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
99 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
100 * <li>VERSION the version of the jalview build</li>
101 * <li>BUILD_DATE date of this build</li>
102 * <li>LATEST_VERSION the latest jalview version advertised on the
103 * www.jalview.org</li>
104 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
106 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
107 * suffix to file</li>
108 * <li>RECENT_URL list of recently retrieved URLs</li>
109 * <li>RECENT_FILE list of recently opened files</li>
110 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
111 * <li>PROXY_SERVER the proxy</li>
112 * <li>PROXY_PORT</li>
113 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
115 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
117 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
118 * collecting usage statistics</li>
119 * <li>SHOW_OVERVIEW boolean for overview window display</li>
120 * <li>ANTI_ALIAS boolean for smooth fonts</li>
121 * <li>RIGHT_ALIGN_IDS boolean</li>
122 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
123 * <li>PAD_GAPS boolean</li>
124 * <li>ID_ITALICS boolean</li>
125 * <li>SHOW_JV_SUFFIX</li>
126 * <li>WRAP_ALIGNMENT</li>
127 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
129 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
130 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
132 * <li>STORED_LINKS list of name|url pairs which user has entered but are not
134 * <li>DEFAULT_LINK name of single url to be used when user double clicks a
135 * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
136 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
137 * jalview.utils.GroupURLLink for more info</li>
138 * <li>DEFAULT_BROWSER for unix</li>
139 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
141 * <li>VERSION_CHECK (true) check for the latest release version from
142 * www.jalview.org (or the alias given by the www.jalview.org property)</li>
143 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
145 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
147 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
148 * displayed as '.'</li>
149 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
150 * order of a newly displayed tree</li>
151 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
152 * sequence ID strings before attempting retrieval from any datasource</li>
153 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
155 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
156 * in the alignment.</li>
157 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
159 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
161 * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
162 * logo normalised to row height rather than histogram height.</li>
163 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
164 * respond to selections made in other alignments containing the same sequences.
166 * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
167 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
168 * warning dialog box is displayed.</li>
169 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
170 * when shading by annotation</li>
171 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
172 * when shading by annotation</li>
173 * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
174 * requests to be redirected to a mirror of http://www.jalview.org</li>
175 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
176 * alignment figure to accommodate even the longest sequence ID or annotation
178 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
179 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
180 * will override this).</li>
181 * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
183 * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
184 * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
186 * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
188 * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
190 * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
191 * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
195 * Deprecated settings:
198 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
199 * startup (JWS1 services only)</li>
200 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
201 * (JWS1 services only)</li>
202 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
203 * services in the desktop GUI</li>
204 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
205 * panel in web service preferences</li>
209 * @version $Revision$
214 * property giving log4j level for CASTOR loggers
216 public static final String CASTORLOGLEVEL = "logs.Castor.level";
219 * property giving log4j level for AXIS loggers
221 public static final String AXISLOGLEVEL = "logs.Axis.level";
224 * property giving log4j level for Jalview Log
226 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
231 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
232 .getProperty("user.home") + File.separatorChar
233 + ".sifts_downloads" + File.separatorChar;
235 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
237 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
240 * Identifiers.org download settings
242 private static final String ID_ORG_FILE = System.getProperty("user.home")
243 + File.separatorChar + ".identifiers.org.ids.json";
246 * Allowed values are PDB or mmCIF
248 private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
251 private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
255 * a date formatter using a fixed (rather than the user's) locale;
256 * this ensures that date properties can be written and re-read successfully
257 * even if the user changes their locale setting
259 private static final DateFormat date_format = SimpleDateFormat
260 .getDateTimeInstance(SimpleDateFormat.MEDIUM,
261 SimpleDateFormat.MEDIUM, Locale.UK);
264 * Initialises the Jalview Application Log
266 public static Logger log;
268 /** Jalview Properties */
269 private static Properties applicationProperties = new Properties()
271 // override results in properties output in alphabetical order
273 public synchronized Enumeration<Object> keys()
275 return Collections.enumeration(new TreeSet<>(super.keySet()));
279 /** Default file is ~/.jalview_properties */
280 static String propertiesFile;
282 private static boolean propsAreReadOnly = Platform.isJS();
284 private final static String JS_PROPERTY_PREFIX = "jalview_";
286 public static void initLogger()
294 // TODO: redirect stdout and stderr here in order to grab the output of
297 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
299 ap.setName("JalviewLogger");
300 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
302 Logger laxis = Logger.getLogger("org.apache.axis");
303 Logger lcastor = Logger.getLogger("org.exolab.castor");
304 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
306 laxis.setLevel(Level.toLevel(
307 Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
308 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
309 Level.INFO.toString())));
310 lcastor = Logger.getLogger("org.exolab.castor.xml");
311 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
312 Level.INFO.toString())));
313 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
314 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
315 // Level.INFO.toString())));
316 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
317 .getDefault("logs.Jalview.level", Level.INFO.toString())));
318 // laxis.addAppender(ap);
319 // lcastor.addAppender(ap);
320 // jalview.bin.Cache.log.addAppender(ap);
321 // Tell the user that debug is enabled
322 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
323 } catch (Exception ex)
325 System.err.println("Problems initializing the log4j system\n");
326 ex.printStackTrace(System.err);
331 * Loads properties from the given properties file. Any existing properties
334 public static void loadProperties(String propsFile)
336 /* for JalviewJS should be
341 loadPropertiesImpl(propsFile);
345 private /* JalviewJS should not be static */
347 void loadPropertiesImpl(String propsFile)
350 propertiesFile = propsFile;
351 if (propsFile == null && !propsAreReadOnly)
353 propertiesFile = System.getProperty("user.home") + File.separatorChar
354 + ".jalview_properties";
358 // don't corrupt the file we've been given.
359 propsAreReadOnly = true;
362 if (propertiesFile == null)
364 Platform.readInfoProperties(JS_PROPERTY_PREFIX,
365 applicationProperties);
374 fis = new java.net.URL(propertiesFile).openStream();
376 "Loading jalview properties from : " + propertiesFile);
378 "Disabling Jalview writing to user's local properties file.");
379 propsAreReadOnly = true;
381 } catch (Exception ex)
387 fis = new FileInputStream(propertiesFile);
389 applicationProperties.clear();
390 applicationProperties.load(fis);
392 // remove any old build properties
394 deleteBuildProperties();
396 } catch (Exception ex)
398 System.out.println("Error reading properties file: " + ex);
401 if (getDefault("USE_PROXY", false))
403 String proxyServer = getDefault("PROXY_SERVER", ""),
404 proxyPort = getDefault("PROXY_PORT", "8080");
406 System.out.println("Using proxyServer: " + proxyServer
407 + " proxyPort: " + proxyPort);
409 System.setProperty("http.proxyHost", proxyServer);
410 System.setProperty("http.proxyPort", proxyPort);
413 // LOAD THE AUTHORS FROM THE authors.props file
414 String authorDetails = resolveResourceURLFor("/authors.props");
418 if (authorDetails != null)
420 URL localJarFileURL = new URL(authorDetails);
421 InputStream in = localJarFileURL.openStream();
422 applicationProperties.load(in);
425 } catch (Exception ex)
427 System.out.println("Error reading author details: " + ex);
428 authorDetails = null;
430 if (authorDetails == null)
432 applicationProperties.remove("AUTHORS");
433 applicationProperties.remove("AUTHORFNAMES");
434 applicationProperties.remove("YEAR");
437 loadBuildProperties(false);
440 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
442 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
443 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
445 SiftsSettings.setFailSafePIDThreshold(
446 jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
447 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
449 SiftsSettings.setCacheThresholdInDays(
450 jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
451 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
453 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
454 "http://www.jalview.org/services/identifiers"));
455 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
457 StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
458 .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
459 StructureImportSettings
460 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
461 // StructureImportSettings
462 // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
463 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
465 String jnlpVersion = System.getProperty("jalview.version");
467 // jnlpVersion will be null if a latest version check for the channel needs to
469 // Dont do this check if running in headless mode
471 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
472 && (System.getProperty("java.awt.headless") == null || System
473 .getProperty("java.awt.headless").equals("false")))
480 String orgtimeout = System
481 .getProperty("sun.net.client.defaultConnectTimeout");
482 if (orgtimeout == null)
485 System.out.println("# INFO: Setting default net timeout to "
486 + orgtimeout + " seconds.");
488 String remoteVersion = null;
491 System.setProperty("sun.net.client.defaultConnectTimeout",
493 java.net.URL url = new java.net.URL(Cache
494 .getDefault("www.jalview.org", "http://www.jalview.org")
495 + "/webstart/jalview.jnlp");
496 BufferedReader in = new BufferedReader(
497 new InputStreamReader(url.openStream()));
499 while ((line = in.readLine()) != null)
501 if (line.indexOf("jalview.version") == -1)
506 line = line.substring(line.indexOf("value=") + 7);
507 line = line.substring(0, line.lastIndexOf("\""));
508 remoteVersion = line;
511 } catch (Exception ex)
514 "Non-fatal exception when checking version at www.jalview.org :");
515 System.out.println(ex);
516 remoteVersion = getProperty("VERSION");
518 System.setProperty("sun.net.client.defaultConnectTimeout",
521 setProperty("LATEST_VERSION", remoteVersion);
527 if (jnlpVersion != null)
529 setProperty("LATEST_VERSION", jnlpVersion);
533 applicationProperties.remove("LATEST_VERSION");
537 // LOAD USERDEFINED COLOURS
538 Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
539 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
544 * construct a resource URL for the given absolute resource pathname
546 * @param resourcePath
549 private static String resolveResourceURLFor(String resourcePath)
552 if (Platform.isJS() || !Cache.class.getProtectionDomain()
553 .getCodeSource().getLocation().toString().endsWith(".jar"))
557 url = Cache.class.getResource(resourcePath).toString();
558 } catch (Exception ex)
560 System.err.println("Failed to resolve resource " + resourcePath + ": "
566 url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
567 .getLocation().toString().concat("!" + resourcePath));
572 public static void loadBuildProperties(boolean reportVersion)
574 String codeInstallation = getProperty("INSTALLATION");
575 boolean printVersion = codeInstallation == null;
578 * read build properties - from the Jalview jar for a Java distribution,
579 * or from codebase file in test or JalviewJS context
583 String buildDetails = resolveResourceURLFor("/.build_properties");
584 URL localJarFileURL = new URL(buildDetails);
585 InputStream in = localJarFileURL.openStream();
586 applicationProperties.load(in);
588 } catch (Exception ex)
590 System.out.println("Error reading build details: " + ex);
591 applicationProperties.remove("VERSION");
593 String codeVersion = getProperty("VERSION");
594 codeInstallation = getProperty("INSTALLATION");
596 if (codeVersion == null)
598 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
599 codeVersion = "Test";
600 codeInstallation = "";
604 codeInstallation = " (" + codeInstallation + ")";
606 setProperty("VERSION", codeVersion);
607 new BuildDetails(codeVersion, null, codeInstallation);
608 if (printVersion && reportVersion)
611 .println("Jalview Version: " + codeVersion + codeInstallation);
615 private static void deleteBuildProperties()
617 applicationProperties.remove("LATEST_VERSION");
618 applicationProperties.remove("VERSION");
619 applicationProperties.remove("AUTHORS");
620 applicationProperties.remove("AUTHORFNAMES");
621 applicationProperties.remove("YEAR");
622 applicationProperties.remove("BUILD_DATE");
623 applicationProperties.remove("INSTALLATION");
627 * Gets Jalview application property of given key. Returns null if key not
633 * @return Property value
635 public static String getProperty(String key)
637 String prop = /* for JalviewJS should be
642 applicationProperties.getProperty(key);
643 // if (prop == null && Platform.isJS())
645 // prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
646 // + "_" + JS_PROPERTY_PREFIX + key);
652 * These methods are used when checking if the saved preference is different
653 * to the default setting
656 public static boolean getDefault(String property, boolean def)
658 String string = getProperty(property);
661 def = Boolean.valueOf(string).booleanValue();
667 public static int getDefault(String property, int def)
669 String string = getProperty(property);
674 def = Integer.parseInt(string);
675 } catch (NumberFormatException e)
677 System.out.println("Error parsing int property '" + property
678 + "' with value '" + string + "'");
686 * Answers the value of the given property, or the supplied default value if
687 * the property is not set
689 public static String getDefault(String property, String def)
691 String value = getProperty(property);
692 return value == null ? def : value;
696 * Stores property in the file "HOME_DIR/.jalview_properties"
701 * String value of property
703 * @return previous value of property (or null)
705 public static Object setProperty(String key, String obj)
707 Object oldValue = null;
710 oldValue = applicationProperties.setProperty(key, obj);
711 if (propertiesFile != null && !propsAreReadOnly)
713 FileOutputStream out = new FileOutputStream(propertiesFile);
714 applicationProperties.store(out, "---JalviewX Properties File---");
717 } catch (Exception ex)
720 "Error setting property: " + key + " " + obj + "\n" + ex);
726 * Removes the specified property from the jalview properties file
730 public static void removeProperty(String key)
732 /* for JalviewJS should be
737 removePropertyImpl(key, true);
741 * Removes the named property for the running application, without saving the
744 * BH noting that ColourMenuHelper calls this. If the intent is to save,
745 * then simply chanet that call to removeProperty(key).
749 public static void removePropertyNoSave(String key)
751 /* for JalviewJS should be
756 removePropertyImpl(key, false);
760 * Removes the named property, and optionally saves the current properties to
766 private /* JalviewJS should not be static */
768 void removePropertyImpl(String key, boolean andSave)
770 applicationProperties.remove(key);
776 * save the properties to the jalview properties path
778 public static void saveProperties()
780 if (!propsAreReadOnly)
784 FileOutputStream out = new FileOutputStream(propertiesFile);
785 applicationProperties.store(out, "---JalviewX Properties File---");
787 } catch (Exception ex)
789 System.out.println("Error saving properties: " + ex);
795 * internal vamsas class discovery state
797 private static int vamsasJarsArePresent = -1;
800 * Searches for vamsas client classes on class path.
802 * @return true if vamsas client is present on classpath
804 public static boolean vamsasJarsPresent()
806 if (vamsasJarsArePresent == -1)
810 if (jalview.jbgui.GDesktop.class.getClassLoader()
811 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
813 jalview.bin.Cache.log.debug(
814 "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
815 vamsasJarsArePresent = 1;
816 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
817 lvclient.setLevel(Level.toLevel(Cache
818 .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
820 lvclient.addAppender(log.getAppender("JalviewLogger"));
821 // Tell the user that debug is enabled
822 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
824 } catch (Exception e)
826 vamsasJarsArePresent = 0;
827 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
830 return (vamsasJarsArePresent > 0);
834 * internal vamsas class discovery state
836 private static int groovyJarsArePresent = -1;
839 * Searches for vamsas client classes on class path.
841 * @return true if vamsas client is present on classpath
843 public static boolean groovyJarsPresent()
845 if (groovyJarsArePresent == -1)
849 if (Cache.class.getClassLoader()
850 .loadClass("groovy.lang.GroovyObject") != null)
852 jalview.bin.Cache.log.debug(
853 "Found Groovy (groovy.lang.GroovyObject can be loaded)");
854 groovyJarsArePresent = 1;
855 Logger lgclient = Logger.getLogger("groovy");
856 lgclient.setLevel(Level.toLevel(Cache
857 .getDefault("logs.Groovy.Level", Level.INFO.toString())));
859 lgclient.addAppender(log.getAppender("JalviewLogger"));
860 // Tell the user that debug is enabled
861 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
865 groovyJarsArePresent = 0;
866 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
867 } catch (Exception e)
869 groovyJarsArePresent = 0;
870 jalview.bin.Cache.log.debug("Groovy Classes are not present");
873 return (groovyJarsArePresent > 0);
877 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
880 protected static Object tracker = null;
882 protected static Class trackerfocus = null;
884 protected static Class jgoogleanalyticstracker = null;
887 * Initialise the google tracker if it is not done already.
889 public static void initGoogleTracker()
893 if (jgoogleanalyticstracker == null)
895 // try to get the tracker class
898 jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
899 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
900 trackerfocus = Cache.class.getClassLoader()
901 .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
902 } catch (Exception e)
905 "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
907 jgoogleanalyticstracker = null;
912 // now initialise tracker
913 Exception re = null, ex = null;
915 String vrs = "No Version Accessible";
918 // Google analytics tracking code for Library Finder
919 tracker = jgoogleanalyticstracker
920 .getConstructor(new Class[]
921 { String.class, String.class, String.class })
922 .newInstance(new Object[]
924 (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
925 + jalview.bin.Cache.getDefault("BUILD_DATE",
928 jgoogleanalyticstracker
929 .getMethod("trackAsynchronously", new Class[]
931 .invoke(tracker, new Object[]
932 { trackerfocus.getConstructor(new Class[] { String.class })
933 .newInstance(new Object[]
934 { "Application Started." }) });
935 } catch (RuntimeException e)
938 } catch (Exception e)
945 if (re != null || ex != null || err != null)
951 log.debug("Caught runtime exception in googletracker init:",
957 "Failed to initialise GoogleTracker for Jalview Desktop with version "
964 "Whilst initing GoogleTracker for Jalview Desktop version "
974 "Debug: Caught runtime exception in googletracker init:"
976 re.printStackTrace();
981 "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
983 ex.printStackTrace();
989 "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
991 err.printStackTrace();
997 log.debug("Successfully initialised tracker.");
1003 * get the user's default colour if available
1009 public static Color getDefaultColour(String property, Color defcolour)
1011 String colprop = getProperty(property);
1012 if (colprop == null)
1016 Color col = ColorUtils.parseColourString(colprop);
1019 log.warn("Couldn't parse '" + colprop + "' as a colour for "
1022 return (col == null) ? defcolour : col;
1026 * store a colour as a Jalview user default property
1031 public static void setColourProperty(String property, Color colour)
1033 setProperty(property, jalview.util.Format.getHexString(colour));
1037 * Stores a formatted date in a jalview property, using a fixed locale.
1039 * @param propertyName
1041 * @return the formatted date string
1043 public static String setDateProperty(String propertyName, Date date)
1045 String formatted = date_format.format(date);
1046 setProperty(propertyName, formatted);
1051 * Reads a date stored in a Jalview property, parses it (using a fixed locale
1052 * format) and returns as a Date, or null if parsing fails
1054 * @param propertyName
1058 public static Date getDateProperty(String propertyName)
1060 String val = getProperty(propertyName);
1065 return date_format.parse(val);
1066 } catch (Exception ex)
1068 System.err.println("Invalid or corrupt date in property '"
1069 + propertyName + "' : value was '" + val + "'");
1076 * get and parse a property as an integer. send any parsing problems to
1080 * @return null or Integer
1082 public static Integer getIntegerProperty(String property)
1084 String val = getProperty(property);
1085 if (val != null && (val = val.trim()).length() > 0)
1089 return Integer.valueOf(val);
1090 } catch (NumberFormatException x)
1092 System.err.println("Invalid integer in property '" + property
1093 + "' (value was '" + val + "')");
1100 * Set the specified value, or remove it if null or empty. Does not save the
1106 public static void setOrRemove(String propName, String value)
1108 if (propName == null)
1112 if (value == null || value.trim().length() < 1)
1114 Cache.applicationProperties.remove(propName);
1118 Cache.applicationProperties.setProperty(propName, value);
1123 * Loads in user colour schemes from files.
1126 * a '|'-delimited list of file paths
1128 public static void initUserColourSchemes(String files)
1130 if (files == null || files.length() == 0)
1135 // In case colours can't be loaded, we'll remove them
1136 // from the default list here.
1137 StringBuffer coloursFound = new StringBuffer();
1138 StringTokenizer st = new StringTokenizer(files, "|");
1139 while (st.hasMoreElements())
1141 String file = st.nextToken();
1144 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1147 if (coloursFound.length() > 0)
1149 coloursFound.append("|");
1151 coloursFound.append(file);
1152 ColourSchemes.getInstance().registerColourScheme(ucs);
1154 } catch (Exception ex)
1156 System.out.println("Error loading User ColourFile\n" + ex);
1159 if (!files.equals(coloursFound.toString()))
1161 if (coloursFound.toString().length() > 1)
1163 /* for JalviewJS should be
1168 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1169 coloursFound.toString());
1173 applicationProperties
1174 .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1180 * Initial logging information helper for various versions output
1184 * @param defaultValue
1186 private static void appendIfNotNull(StringBuilder sb, String prefix,
1187 String value, String suffix, String defaultValue)
1189 if (value == null && defaultValue == null)
1193 String line = prefix + (value != null ? value : defaultValue) + suffix;
1199 * @return Jalview version, build details and JVM platform version for console
1201 public static String getVersionDetailsForConsole()
1203 StringBuilder sb = new StringBuilder();
1204 sb.append("Jalview Version: " + jalview.bin.Cache.getDefault("VERSION", "TEST"));
1206 sb.append("Jalview Installation: "
1207 + jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
1209 sb.append("Build Date: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
1211 sb.append("Java version: " + System.getProperty("java.version"));
1213 sb.append(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version"));
1215 appendIfNotNull(sb, "Install4j version: ",
1216 System.getProperty("sys.install4jVersion"), "\n", null);
1217 appendIfNotNull(sb, "Install4j template version: ",
1218 System.getProperty("installer_template_version"), "\n", null);
1219 appendIfNotNull(sb, "Launcher version: ",
1220 System.getProperty("launcher_version"), "\n", null);
1221 if (jalview.bin.Cache.getDefault("VERSION", "TEST").equals("DEVELOPMENT")) {
1222 appendIfNotNull(sb, "Getdown appdir: ",
1223 System.getProperty("getdownappdir"), "\n", null);
1224 appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
1227 return sb.toString();
1232 * @return build details as reported in splashscreen
1234 public static String getBuildDetailsForSplash()
1236 // consider returning more human friendly info
1237 // eg 'built from Source' or update channel
1238 return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
1243 * For AppletParams and Preferences ok_actionPerformed and startupFileTextfield_mouseClicked
1245 * Sets a property value for the running application, without saving it to the
1251 public static void setPropertyNoSave(String key, String obj)
1253 /* for JalviewJS should be
1258 setPropertyImpl(key, obj, false);
1262 * Sets a property value, and optionally also saves the current properties to
1270 private /* for JalviewJS should not be static */ static Object setPropertyImpl(String key, String obj, boolean andSave)
1272 Object oldValue = null;
1275 oldValue = applicationProperties.setProperty(key, obj);
1276 if (andSave && !propsAreReadOnly && propertiesFile != null)
1278 FileOutputStream out = new FileOutputStream(propertiesFile);
1279 applicationProperties.store(out, "---JalviewX Properties File---");
1282 } catch (Exception ex)
1285 "Error setting property: " + key + " " + obj + "\n" + ex);