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;
25 import java.io.FileInputStream;
26 import java.io.FileOutputStream;
27 import java.io.InputStream;
28 import java.io.InputStreamReader;
30 import java.text.DateFormat;
31 import java.text.SimpleDateFormat;
32 import java.util.Collections;
33 import java.util.Date;
34 import java.util.Enumeration;
35 import java.util.Locale;
36 import java.util.Properties;
37 import java.util.StringTokenizer;
38 import java.util.TreeSet;
40 import org.apache.log4j.ConsoleAppender;
41 import org.apache.log4j.Level;
42 import org.apache.log4j.Logger;
43 import org.apache.log4j.SimpleLayout;
45 import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
46 import jalview.datamodel.PDBEntry;
47 import jalview.gui.UserDefinedColours;
48 import jalview.schemes.ColourSchemeLoader;
49 import jalview.schemes.ColourSchemes;
50 import jalview.schemes.UserColourScheme;
51 import jalview.structure.StructureImportSettings;
52 import jalview.urls.IdOrgSettings;
53 import jalview.util.ColorUtils;
54 import jalview.util.Platform;
55 import jalview.ws.sifts.SiftsSettings;
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 $Revision$
211 public class Cache implements ApplicationSingletonI
220 * In Java, this will be a static field instance, which will be
221 * application-specific; in JavaScript it will be an applet-specific instance
222 * tied to the applet's ThreadGroup.
226 public static Cache getInstance()
228 return (Cache) ApplicationSingletonProvider.getInstance(Cache.class);
232 * property giving log4j level for CASTOR loggers
234 public static final String CASTORLOGLEVEL = "logs.Castor.level";
237 * property giving log4j level for AXIS loggers
239 public static final String AXISLOGLEVEL = "logs.Axis.level";
242 * property giving log4j level for Jalview Log
244 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
249 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = Platform.getUserPath(".sifts_downloads/");
251 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
253 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
256 * Identifiers.org download settings
258 private static final String ID_ORG_FILE = Platform.getUserPath(".identifiers.org.ids.json");
261 * Allowed values are PDB or mmCIF
263 private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
266 private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
270 * a date formatter using a fixed (rather than the user's) locale;
271 * this ensures that date properties can be written and re-read successfully
272 * even if the user changes their locale setting
274 private static final DateFormat date_format = SimpleDateFormat
275 .getDateTimeInstance(SimpleDateFormat.MEDIUM,
276 SimpleDateFormat.MEDIUM, Locale.UK);
279 * Initialises the Jalview Application Log
281 public static Logger log;
283 /** Jalview Properties */
284 private Properties applicationProperties = new Properties()
286 // override results in properties output in alphabetical order
288 public synchronized Enumeration<Object> keys()
290 return Collections.enumeration(new TreeSet<>(super.keySet()));
294 /** Default file is ~/.jalview_properties */
295 static String propertiesFile;
297 private static boolean propsAreReadOnly = Platform.isJS();
299 private final static String JS_PROPERTY_PREFIX = "jalview_";
301 public static void initLogger()
309 // TODO: redirect stdout and stderr here in order to grab the output of
312 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
314 ap.setName("JalviewLogger");
315 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
317 Logger laxis = Logger.getLogger("org.apache.axis");
318 Logger lcastor = Logger.getLogger("org.exolab.castor");
319 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
321 laxis.setLevel(Level.toLevel(
322 Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
323 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
324 Level.INFO.toString())));
325 lcastor = Logger.getLogger("org.exolab.castor.xml");
326 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
327 Level.INFO.toString())));
328 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
329 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
330 // Level.INFO.toString())));
331 // we shouldn't need to do this
332 org.apache.log4j.Logger.getRootLogger().setLevel(org.apache.log4j.Level.INFO);
334 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
335 .getDefault("logs.Jalview.level", Level.INFO.toString())));
336 // laxis.addAppender(ap);
337 // lcastor.addAppender(ap);
338 // jalview.bin.Cache.log.addAppender(ap);
339 // Tell the user that debug is enabled
340 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
341 } catch (Exception ex)
343 System.err.println("Problems initializing the log4j system\n");
344 ex.printStackTrace(System.err);
349 * Loads properties from the given properties file. Any existing properties
352 public static void loadProperties(String propsFile)
355 getInstance().loadPropertiesImpl(propsFile);
359 private void loadPropertiesImpl(String propsFile)
362 propertiesFile = propsFile;
363 if (propsFile == null && !propsAreReadOnly)
365 propertiesFile = Platform.getUserPath(".jalview_properties");
369 // don't corrupt the file we've been given.
370 propsAreReadOnly = true;
373 if (propertiesFile == null)
375 Platform.readInfoProperties(JS_PROPERTY_PREFIX,
376 applicationProperties);
385 fis = new java.net.URL(propertiesFile).openStream();
387 "Loading jalview properties from : " + propertiesFile);
389 "Disabling Jalview writing to user's local properties file.");
390 propsAreReadOnly = true;
392 } catch (Exception ex)
398 fis = new FileInputStream(propertiesFile);
400 applicationProperties.clear();
401 applicationProperties.load(fis);
403 // remove any old build properties
405 deleteBuildProperties();
407 } catch (Exception ex)
409 System.out.println("Error reading properties file: " + ex);
412 if (getDefault("USE_PROXY", false))
414 String proxyServer = getDefault("PROXY_SERVER", ""),
415 proxyPort = getDefault("PROXY_PORT", "8080");
417 System.out.println("Using proxyServer: " + proxyServer
418 + " proxyPort: " + proxyPort);
420 System.setProperty("http.proxyHost", proxyServer);
421 System.setProperty("http.proxyPort", proxyPort);
424 // LOAD THE AUTHORS FROM THE authors.props file
425 String authorDetails = resolveResourceURLFor("/authors.props");
429 if (authorDetails != null)
431 URL localJarFileURL = new URL(authorDetails);
432 InputStream in = localJarFileURL.openStream();
433 applicationProperties.load(in);
436 } catch (Exception ex)
438 System.out.println("Error reading author details: " + ex);
439 authorDetails = null;
441 if (authorDetails == null)
443 applicationProperties.remove("AUTHORS");
444 applicationProperties.remove("AUTHORFNAMES");
445 applicationProperties.remove("YEAR");
448 loadBuildProperties(false);
451 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
453 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
454 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
456 SiftsSettings.setFailSafePIDThreshold(
457 jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
458 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
460 SiftsSettings.setCacheThresholdInDays(
461 jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
462 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
464 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
465 "http://www.jalview.org/services/identifiers"));
466 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
468 StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
469 .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
470 StructureImportSettings
471 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
472 // StructureImportSettings
473 // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
474 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
476 String jnlpVersion = System.getProperty("jalview.version");
478 // jnlpVersion will be null if a latest version check for the channel needs
481 // Dont do this check if running in headless mode
483 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
484 && (System.getProperty("java.awt.headless") == null || System
485 .getProperty("java.awt.headless").equals("false")))
492 String orgtimeout = System
493 .getProperty("sun.net.client.defaultConnectTimeout");
494 if (orgtimeout == null)
497 System.out.println("# INFO: Setting default net timeout to "
498 + orgtimeout + " seconds.");
500 String remoteVersion = null;
503 System.setProperty("sun.net.client.defaultConnectTimeout",
505 java.net.URL url = new java.net.URL(Cache
506 .getDefault("www.jalview.org", "http://www.jalview.org")
507 + "/webstart/jalview.jnlp");
508 BufferedReader in = new BufferedReader(
509 new InputStreamReader(url.openStream()));
511 while ((line = in.readLine()) != null)
513 if (line.indexOf("jalview.version") == -1)
518 line = line.substring(line.indexOf("value=") + 7);
519 line = line.substring(0, line.lastIndexOf("\""));
520 remoteVersion = line;
523 } catch (Exception ex)
526 "Non-fatal exception when checking version at www.jalview.org :");
527 System.out.println(ex);
528 remoteVersion = getProperty("VERSION");
530 System.setProperty("sun.net.client.defaultConnectTimeout",
533 setProperty("LATEST_VERSION", remoteVersion);
539 if (jnlpVersion != null)
541 setProperty("LATEST_VERSION", jnlpVersion);
545 applicationProperties.remove("LATEST_VERSION");
549 // LOAD USERDEFINED COLOURS
550 Cache.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
551 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
556 * construct a resource URL for the given absolute resource pathname
558 * @param resourcePath
561 private static String resolveResourceURLFor(String resourcePath)
564 if (Platform.isJS() || !Cache.class.getProtectionDomain()
565 .getCodeSource().getLocation().toString().endsWith(".jar"))
569 url = Cache.class.getResource(resourcePath).toString();
570 } catch (Exception ex)
572 System.err.println("Failed to resolve resource " + resourcePath
573 + ": " + ex.getMessage());
578 url = "jar:".concat(Cache.class.getProtectionDomain().getCodeSource()
579 .getLocation().toString().concat("!" + resourcePath));
584 public void loadBuildProperties(boolean reportVersion)
586 String codeInstallation = getProperty("INSTALLATION");
587 boolean printVersion = codeInstallation == null;
590 * read build properties - from the Jalview jar for a Java distribution,
591 * or from codebase file in test or JalviewJS context
595 String buildDetails = resolveResourceURLFor("/.build_properties");
596 URL localJarFileURL = new URL(buildDetails);
597 InputStream in = localJarFileURL.openStream();
598 applicationProperties.load(in);
600 } catch (Exception ex)
602 System.out.println("Error reading build details: " + ex);
603 applicationProperties.remove("VERSION");
605 String codeVersion = getProperty("VERSION");
606 codeInstallation = getProperty("INSTALLATION");
608 if (codeVersion == null)
610 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
611 codeVersion = "Test";
612 codeInstallation = "";
616 codeInstallation = " (" + codeInstallation + ")";
618 setProperty("VERSION", codeVersion);
619 new BuildDetails(codeVersion, null, codeInstallation);
620 if (printVersion && reportVersion)
623 "Jalview Version: " + codeVersion + codeInstallation);
627 private void deleteBuildProperties()
629 applicationProperties.remove("LATEST_VERSION");
630 applicationProperties.remove("VERSION");
631 applicationProperties.remove("AUTHORS");
632 applicationProperties.remove("AUTHORFNAMES");
633 applicationProperties.remove("YEAR");
634 applicationProperties.remove("BUILD_DATE");
635 applicationProperties.remove("INSTALLATION");
639 * Gets Jalview application property of given key. Returns null if key not
645 * @return Property value
647 public static String getProperty(String key)
649 String prop = getInstance().applicationProperties.getProperty(key);
650 // if (prop == null && Platform.isJS())
652 // prop = applicationProperties.getProperty(Platform.getUniqueAppletID()
653 // + "_" + JS_PROPERTY_PREFIX + key);
659 * These methods are used when checking if the saved preference is different
660 * to the default setting
663 public static boolean getDefault(String property, boolean def)
665 String string = getProperty(property);
668 def = Boolean.valueOf(string).booleanValue();
674 public static int getDefault(String property, int def)
676 String string = getProperty(property);
681 def = Integer.parseInt(string);
682 } catch (NumberFormatException e)
684 System.out.println("Error parsing int property '" + property
685 + "' with value '" + string + "'");
693 * Answers the value of the given property, or the supplied default value if
694 * the property is not set
696 public static String getDefault(String property, String def)
698 String value = getProperty(property);
699 return value == null ? def : value;
703 * Stores property in the file "HOME_DIR/.jalview_properties"
708 * String value of property
710 * @return previous value of property (or null)
712 public static Object setProperty(String key, String obj)
714 return getInstance().setPropertyImpl(key, obj, true);
718 * Removes the specified property from the jalview properties file
722 public static void removeProperty(String key)
724 getInstance().removePropertyImpl(key, true);
728 * Removes the named property for the running application, without saving the
731 * BH noting that ColourMenuHelper calls this. If the intent is to save, then
732 * simply chanet that call to removeProperty(key).
736 public static void removePropertyNoSave(String key)
741 removePropertyImpl(key, false);
745 * Removes the named property, and optionally saves the current properties to
751 private void removePropertyImpl(String key, boolean andSave)
753 applicationProperties.remove(key);
759 * save the properties to the jalview properties path
761 public static void saveProperties()
763 getInstance().savePropertiesImpl();
767 * save the properties to the jalview properties path
769 private void savePropertiesImpl()
772 if (!propsAreReadOnly)
776 FileOutputStream out = new FileOutputStream(propertiesFile);
777 applicationProperties.store(out, "---JalviewX Properties File---");
779 } catch (Exception ex)
781 System.out.println("Error saving properties: " + ex);
787 * internal vamsas class discovery state
789 private static int vamsasJarsArePresent = -1;
792 * Searches for vamsas client classes on class path.
794 * @return true if vamsas client is present on classpath
796 public static boolean vamsasJarsPresent()
798 if (vamsasJarsArePresent == -1)
802 if (jalview.jbgui.GDesktop.class.getClassLoader()
803 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
805 jalview.bin.Cache.log.debug(
806 "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
807 vamsasJarsArePresent = 1;
808 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
809 lvclient.setLevel(Level.toLevel(Cache
810 .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
812 lvclient.addAppender(log.getAppender("JalviewLogger"));
813 // Tell the user that debug is enabled
814 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
816 } catch (Exception e)
818 vamsasJarsArePresent = 0;
819 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
822 return (vamsasJarsArePresent > 0);
826 * internal vamsas class discovery state
828 private static int groovyJarsArePresent = -1;
831 * Searches for vamsas client classes on class path.
833 * @return true if vamsas client is present on classpath
835 public static boolean groovyJarsPresent()
837 if (groovyJarsArePresent == -1)
841 if (Cache.class.getClassLoader()
842 .loadClass("groovy.lang.GroovyObject") != null)
844 jalview.bin.Cache.log.debug(
845 "Found Groovy (groovy.lang.GroovyObject can be loaded)");
846 groovyJarsArePresent = 1;
847 Logger lgclient = Logger.getLogger("groovy");
848 lgclient.setLevel(Level.toLevel(Cache
849 .getDefault("logs.Groovy.Level", Level.INFO.toString())));
851 lgclient.addAppender(log.getAppender("JalviewLogger"));
852 // Tell the user that debug is enabled
853 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
857 groovyJarsArePresent = 0;
858 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
859 } catch (Exception e)
861 groovyJarsArePresent = 0;
862 jalview.bin.Cache.log.debug("Groovy Classes are not present");
865 return (groovyJarsArePresent > 0);
869 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
872 protected static Object tracker = null;
874 protected static Class trackerfocus = null;
876 protected static Class jgoogleanalyticstracker = null;
879 * Initialise the google tracker if it is not done already.
881 public static void initGoogleTracker()
885 if (jgoogleanalyticstracker == null)
887 // try to get the tracker class
890 jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
891 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
892 trackerfocus = Cache.class.getClassLoader()
893 .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
894 } catch (Exception e)
897 "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
899 jgoogleanalyticstracker = null;
904 // now initialise tracker
905 Exception re = null, ex = null;
907 String vrs = "No Version Accessible";
910 // Google analytics tracking code for Library Finder
911 tracker = jgoogleanalyticstracker
912 .getConstructor(new Class[]
913 { String.class, String.class, String.class })
914 .newInstance(new Object[]
916 (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
917 + jalview.bin.Cache.getDefault("BUILD_DATE",
920 jgoogleanalyticstracker
921 .getMethod("trackAsynchronously", new Class[]
923 .invoke(tracker, new Object[]
924 { trackerfocus.getConstructor(new Class[] { String.class })
925 .newInstance(new Object[]
926 { "Application Started." }) });
927 } catch (RuntimeException e)
930 } catch (Exception e)
937 if (re != null || ex != null || err != null)
943 log.debug("Caught runtime exception in googletracker init:",
949 "Failed to initialise GoogleTracker for Jalview Desktop with version "
956 "Whilst initing GoogleTracker for Jalview Desktop version "
966 "Debug: Caught runtime exception in googletracker init:"
968 re.printStackTrace();
973 "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
975 ex.printStackTrace();
981 "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
983 err.printStackTrace();
989 log.debug("Successfully initialised tracker.");
995 * get the user's default colour if available
1001 public static Color getDefaultColour(String property, Color defcolour)
1003 String colprop = getProperty(property);
1004 if (colprop == null)
1008 Color col = ColorUtils.parseColourString(colprop);
1011 log.warn("Couldn't parse '" + colprop + "' as a colour for "
1014 return (col == null) ? defcolour : col;
1018 * store a colour as a Jalview user default property
1023 public static void setColourPropertyNoSave(String property, Color colour)
1025 setPropertyNoSave(property, jalview.util.Format.getHexString(colour));
1029 * Stores a formatted date in a jalview property, using a fixed locale.
1031 * @param propertyName
1033 * @return the formatted date string
1035 public static String setDateProperty(String propertyName, Date date)
1037 String formatted = date_format.format(date);
1038 setProperty(propertyName, formatted);
1043 * Reads a date stored in a Jalview property, parses it (using a fixed locale
1044 * format) and returns as a Date, or null if parsing fails
1046 * @param propertyName
1050 public static Date getDateProperty(String propertyName)
1052 String val = getProperty(propertyName);
1058 if ((val = val.trim()).indexOf(",") < 0 && val.indexOf("-") >= 0 && val.indexOf(" ") == val.lastIndexOf(" ")) {
1059 val = val.replace(" ",", ").replace('-',' ');
1061 Date date = date_format.parse(val);
1063 } catch (Exception ex)
1065 System.err.println("Invalid or corrupt date in property '"
1066 + propertyName + "' : value was '" + val + "'");
1073 * get and parse a property as an integer. send any parsing problems to
1077 * @return null or Integer
1079 public static Integer getIntegerProperty(String property)
1081 String val = getProperty(property);
1082 if (val != null && (val = val.trim()).length() > 0)
1086 return Integer.valueOf(val);
1087 } catch (NumberFormatException x)
1089 System.err.println("Invalid integer in property '" + property
1090 + "' (value was '" + val + "')");
1097 * Set the specified value, or remove it if null or empty. Does not save the
1103 public static void setOrRemove(String propName, String value)
1105 if (propName == null)
1109 if (value == null || value.trim().length() < 1)
1111 getInstance().applicationProperties.remove(propName);
1115 getInstance().applicationProperties.setProperty(propName, value);
1120 * Loads in user colour schemes from files.
1123 * a '|'-delimited list of file paths
1125 public static void initUserColourSchemes(String files)
1127 if (files == null || files.length() == 0)
1132 // In case colours can't be loaded, we'll remove them
1133 // from the default list here.
1134 StringBuffer coloursFound = new StringBuffer();
1135 StringTokenizer st = new StringTokenizer(files, "|");
1136 while (st.hasMoreElements())
1138 String file = st.nextToken();
1141 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1144 if (coloursFound.length() > 0)
1146 coloursFound.append("|");
1148 coloursFound.append(file);
1149 ColourSchemes.getInstance().registerColourScheme(ucs);
1151 } catch (Exception ex)
1153 System.out.println("Error loading User ColourFile\n" + ex);
1156 if (!files.equals(coloursFound.toString()))
1158 if (coloursFound.toString().length() > 1)
1160 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1161 coloursFound.toString());
1165 getInstance().applicationProperties
1166 .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1172 * Initial logging information helper for various versions output
1176 * @param defaultValue
1178 private static void appendIfNotNull(StringBuilder sb, String prefix,
1179 String value, String suffix, String defaultValue)
1181 if (value == null && defaultValue == null)
1185 String line = prefix + (value != null ? value : defaultValue) + suffix;
1191 * @return Jalview version, build details and JVM platform version for console
1193 public static String getVersionDetailsForConsole()
1195 StringBuilder sb = new StringBuilder();
1196 sb.append("Jalview Version: "
1197 + jalview.bin.Cache.getDefault("VERSION", "TEST"));
1199 sb.append("Jalview Installation: "
1200 + jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
1202 sb.append("Build Date: "
1203 + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
1205 sb.append("Java version: " + System.getProperty("java.version"));
1207 sb.append(System.getProperty("os.arch") + " "
1208 + System.getProperty("os.name") + " "
1209 + System.getProperty("os.version"));
1211 appendIfNotNull(sb, "Install4j version: ",
1212 System.getProperty("sys.install4jVersion"), "\n", null);
1213 appendIfNotNull(sb, "Install4j template version: ",
1214 System.getProperty("installer_template_version"), "\n", null);
1215 appendIfNotNull(sb, "Launcher version: ",
1216 System.getProperty("launcher_version"), "\n", null);
1217 if (jalview.bin.Cache.getDefault("VERSION", "TEST")
1218 .equals("DEVELOPMENT"))
1220 appendIfNotNull(sb, "Getdown appdir: ",
1221 System.getProperty("getdownappdir"), "\n", null);
1222 appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
1225 return sb.toString();
1230 * @return build details as reported in splashscreen
1232 public static String getBuildDetailsForSplash()
1234 // consider returning more human friendly info
1235 // eg 'built from Source' or update channel
1236 return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
1241 * For AppletParams and Preferences ok_actionPerformed and
1242 * startupFileTextfield_mouseClicked
1244 * Sets a property value for the running application, without saving it to the
1250 public static void setPropertyNoSave(String key, String obj)
1252 getInstance().setPropertyImpl(key, obj, false);
1256 * Sets a property value, and optionally also saves the current properties to
1264 private Object setPropertyImpl(
1265 String key, String obj, boolean andSave)
1267 Object oldValue = null;
1270 oldValue = applicationProperties.setProperty(key, obj);
1271 if (andSave && !propsAreReadOnly && propertiesFile != null)
1273 FileOutputStream out = new FileOutputStream(propertiesFile);
1274 applicationProperties.store(out, "---JalviewX Properties File---");
1277 } catch (Exception ex)
1280 "Error setting property: " + key + " " + obj + "\n" + ex);