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.bin.ApplicationSingletonProvider.ApplicationSingletonI;
24 import jalview.datamodel.PDBEntry;
25 import jalview.gui.Preferences;
26 import jalview.schemes.ColourSchemeLoader;
27 import jalview.schemes.ColourSchemes;
28 import jalview.schemes.UserColourScheme;
29 import jalview.structure.StructureImportSettings;
30 import jalview.urls.IdOrgSettings;
31 import jalview.util.ColorUtils;
32 import jalview.util.Platform;
33 import jalview.ws.sifts.SiftsSettings;
35 import java.awt.Color;
36 import java.io.BufferedReader;
38 import java.io.FileInputStream;
39 import java.io.FileOutputStream;
40 import java.io.InputStream;
41 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 $Revision$
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 private 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 = System
250 .getProperty("user.home") + File.separatorChar
251 + ".sifts_downloads" + File.separatorChar;
253 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
255 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
258 * Identifiers.org download settings
260 private static final String ID_ORG_FILE = System.getProperty("user.home")
261 + File.separatorChar + ".identifiers.org.ids.json";
264 * Allowed values are PDB or mmCIF
266 private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
269 private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
273 * a date formatter using a fixed (rather than the user's) locale;
274 * this ensures that date properties can be written and re-read successfully
275 * even if the user changes their locale setting
277 private static final DateFormat date_format = SimpleDateFormat
278 .getDateTimeInstance(SimpleDateFormat.MEDIUM,
279 SimpleDateFormat.MEDIUM, Locale.UK);
282 * Initialises the Jalview Application Log
284 public static Logger log;
286 /** Jalview Properties */
287 // BH 2019.05.08 was static
288 @SuppressWarnings("serial")
289 private Properties applicationProperties = new Properties()
291 // override results in properties output in alphabetical order
293 public synchronized Enumeration<Object> keys()
295 return Collections.enumeration(new TreeSet<>(super.keySet()));
299 /** Default file is ~/.jalview_properties */
300 private String propertiesFile;
303 * flag to possibly allow properties to be written to a property file
305 private boolean propsAreReadOnly = Platform.isJS();
307 private final static String JS_PROPERTY_PREFIX = "jalview_";
309 public static void initLogger()
317 // TODO: redirect stdout and stderr here in order to grab the output of
320 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
322 ap.setName("JalviewLogger");
323 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
325 Logger laxis = Logger.getLogger("org.apache.axis");
326 Logger lcastor = Logger.getLogger("org.exolab.castor");
327 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
329 laxis.setLevel(Level.toLevel(
330 getDefault("logs.Axis.Level", Level.INFO.toString())));
331 lcastor.setLevel(Level.toLevel(
332 getDefault("logs.Castor.Level", Level.INFO.toString())));
333 lcastor = Logger.getLogger("org.exolab.castor.xml");
334 lcastor.setLevel(Level.toLevel(
335 getDefault("logs.Castor.Level", Level.INFO.toString())));
336 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
337 // lcastor.setLevel(Level.toLevel(getDefault("logs.Castor.Level",
338 // Level.INFO.toString())));
339 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
340 .getDefault("logs.Jalview.level", Level.INFO.toString())));
341 // laxis.addAppender(ap);
342 // lcastor.addAppender(ap);
343 // jalview.bin.Cache.log.addAppender(ap);
344 // Tell the user that debug is enabled
345 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
346 } catch (Exception ex)
348 System.err.println("Problems initializing the log4j system\n");
349 ex.printStackTrace(System.err);
354 * Loads properties from the given properties file. Any existing properties
357 public static void loadProperties(String propsFile)
359 getInstance().loadPropertiesImpl(propsFile);
362 private void loadPropertiesImpl(String propsFile)
364 propertiesFile = propsFile;
365 if (!propsAreReadOnly)
368 if (propsFile == null)
370 propertiesFile = System.getProperty("user.home")
371 + File.separatorChar + ".jalview_properties";
375 // don't corrupt the file we've been given.
376 propsAreReadOnly = true;
380 if (propertiesFile == null)
381 { // BH 2019 read properties from the Info object associated with this
383 Platform.readInfoProperties(JS_PROPERTY_PREFIX,
384 applicationProperties);
393 fis = new java.net.URL(propertiesFile).openStream();
395 "Loading jalview properties from : " + propertiesFile);
397 "Disabling Jalview writing to user's local properties file.");
398 propsAreReadOnly = true;
400 } catch (Exception ex)
406 fis = new FileInputStream(propertiesFile);
408 applicationProperties.clear();
409 applicationProperties.load(fis);
411 // remove any old build properties
413 deleteBuildProperties();
415 } catch (Exception ex)
417 System.out.println("Error reading properties file: " + ex);
420 if (getDefault("USE_PROXY", false))
422 String proxyServer = getDefault("PROXY_SERVER", ""),
423 proxyPort = getDefault("PROXY_PORT", "8080");
425 System.out.println("Using proxyServer: " + proxyServer
426 + " proxyPort: " + proxyPort);
428 System.setProperty("http.proxyHost", proxyServer);
429 System.setProperty("http.proxyPort", proxyPort);
432 // LOAD THE AUTHORS FROM THE authors.props file
433 String authorDetails = (Platform.isJS() ? null
434 : "jar:".concat(Cache.class.getProtectionDomain()
435 .getCodeSource().getLocation().toString()
436 .concat("!/authors.props")));
440 if (authorDetails != null)
442 java.net.URL localJarFileURL = new java.net.URL(authorDetails);
443 InputStream in = localJarFileURL.openStream();
444 applicationProperties.load(in);
447 } catch (Exception ex)
449 System.out.println("Error reading author details: " + ex);
450 authorDetails = null;
452 if (authorDetails == null)
454 applicationProperties.remove("AUTHORS");
455 applicationProperties.remove("AUTHORFNAMES");
456 applicationProperties.remove("YEAR");
459 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
460 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
461 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
462 String buildDetails = (Platform.isJS() ? null
463 : "jar:".concat(Cache.class.getProtectionDomain()
464 .getCodeSource().getLocation().toString()
465 .concat("!/.build_properties")));
466 if (buildDetails != null)
470 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
471 InputStream in = localJarFileURL.openStream();
472 applicationProperties.load(in);
474 } catch (Exception ex)
476 System.out.println("Error reading build details: " + ex);
480 if (buildDetails == null)
482 applicationProperties.remove("VERSION");
484 String jnlpVersion = System.getProperty("jalview.version");
485 String codeVersion = getProperty("VERSION");
486 String codeInstallation = getProperty("INSTALLATION");
487 if (codeVersion == null)
489 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
490 codeVersion = "Test";
491 jnlpVersion = "Test";
492 codeInstallation = "";
496 codeInstallation = " (" + codeInstallation + ")";
498 new BuildDetails(codeVersion, null, codeInstallation);
500 SiftsSettings.setMapWithSifts(getDefault("MAP_WITH_SIFTS", false));
502 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
503 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
505 SiftsSettings.setFailSafePIDThreshold(
506 getDefault("sifts_fail_safe_pid_threshold",
507 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
509 SiftsSettings.setCacheThresholdInDays(
510 getDefault("sifts_cache_threshold_in_days",
511 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
513 IdOrgSettings.setUrl(getDefault(Preferences.ID_ORG_HOSTURL,
514 "http://www.jalview.org/services/identifiers"));
515 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
518 .println("Jalview Version: " + codeVersion + codeInstallation);
520 StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
521 .getDefault(Preferences.PDB_DOWNLOAD_FORMAT, PDB_DOWNLOAD_FORMAT));
522 StructureImportSettings
523 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
524 // StructureImportSettings
525 // .setDefaultPDBFileParser(jalview.bin.getDefault(
526 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
527 // jnlpVersion will be null if we're using InstallAnywhere
528 // Dont do this check if running in headless mode
529 if (jnlpVersion == null && !Jalview.isHeadlessMode()
530 && getDefault("VERSION_CHECK", true))
533 class VersionChecker extends Thread
538 String orgtimeout = System
539 .getProperty("sun.net.client.defaultConnectTimeout");
540 if (orgtimeout == null)
543 System.out.println("# INFO: Setting default net timeout to "
544 + orgtimeout + " seconds.");
546 String remoteVersion = null;
549 System.setProperty("sun.net.client.defaultConnectTimeout",
551 java.net.URL url = new java.net.URL(Cache
552 .getDefault("www.jalview.org", "http://www.jalview.org")
553 + "/webstart/jalview.jnlp");
554 BufferedReader in = new BufferedReader(
555 new InputStreamReader(url.openStream()));
557 while ((line = in.readLine()) != null)
559 if (line.indexOf("jalview.version") == -1)
564 line = line.substring(line.indexOf("value=") + 7);
565 line = line.substring(0, line.lastIndexOf("\""));
566 remoteVersion = line;
569 } catch (Exception ex)
572 "Non-fatal exception when checking version at www.jalview.org :");
573 System.out.println(ex);
574 remoteVersion = getProperty("VERSION");
576 System.setProperty("sun.net.client.defaultConnectTimeout",
579 setProperty("LATEST_VERSION", remoteVersion);
583 VersionChecker vc = new VersionChecker();
588 if (jnlpVersion != null)
590 setProperty("LATEST_VERSION", jnlpVersion);
594 applicationProperties.remove("LATEST_VERSION");
598 setProperty("VERSION", codeVersion);
600 // LOAD USERDEFINED COLOURS
601 initUserColourSchemes(getProperty(Preferences.USER_DEFINED_COLOURS));
604 private void deleteBuildProperties()
606 applicationProperties.remove("LATEST_VERSION");
607 applicationProperties.remove("VERSION");
608 applicationProperties.remove("AUTHORS");
609 applicationProperties.remove("AUTHORFNAMES");
610 applicationProperties.remove("YEAR");
611 applicationProperties.remove("BUILD_DATE");
612 applicationProperties.remove("INSTALLATION");
616 * Gets Jalview application property of given key. Returns null if key not
622 * @return Property value
624 public static String getProperty(String key)
626 return getInstance().applicationProperties.getProperty(key);
630 * These methods are used when checking if the saved preference is different
631 * to the default setting
634 public static boolean getDefault(String property, boolean def)
636 String string = getProperty(property);
639 def = Boolean.valueOf(string).booleanValue();
645 public static int getDefault(String property, int def)
647 String string = getProperty(property);
652 def = Integer.parseInt(string);
653 } catch (NumberFormatException e)
655 System.out.println("Error parsing int property '" + property
656 + "' with value '" + string + "'");
664 * Answers the value of the given property, or the supplied default value if
665 * the property is not set
667 public static String getDefault(String property, String def)
669 String value = getProperty(property);
670 return value == null ? def : value;
674 * Stores property in the file "HOME_DIR/.jalview_properties"
679 * String value of property
681 * @return previous value of property (or null)
683 public static Object setProperty(String key, String obj)
685 return getInstance().setPropertyImpl(key, obj, true);
688 public static void setPropertyNoSave(String key, String obj)
690 getInstance().setPropertyImpl(key, obj, false);
693 private Object setPropertyImpl(String key, String obj, boolean andSave)
695 Object oldValue = null;
698 oldValue = applicationProperties.setProperty(key, obj);
699 if (andSave && !propsAreReadOnly && propertiesFile != null)
701 FileOutputStream out = new FileOutputStream(propertiesFile);
702 applicationProperties.store(out, "---JalviewX Properties File---");
705 } catch (Exception ex)
708 "Error setting property: " + key + " " + obj + "\n" + ex);
714 * remove the specified property from the jalview properties file
718 public static void removeProperty(String key)
720 getInstance().removePropertyImpl(key, true);
723 public static void removePropertyNoSave(String key)
725 getInstance().removePropertyImpl(key, false);
728 private void removePropertyImpl(String key, boolean andSave)
730 applicationProperties.remove(key);
733 savePropertiesImpl();
737 public static void saveProperties()
739 getInstance().savePropertiesImpl();
743 * save the properties to the jalview properties path
745 private void savePropertiesImpl()
747 if (!propsAreReadOnly)
751 FileOutputStream out = new FileOutputStream(propertiesFile);
752 applicationProperties.store(out, "---JalviewX Properties File---");
754 } catch (Exception ex)
756 System.out.println("Error saving properties: " + ex);
761 private final static int UNTESTED = -1;
763 private final static int TRUE = 1;
765 private final static int FALSE = 0;
768 * internal vamsas class discovery state
770 private static int vamsasJarsArePresent = (Platform.isJS() ? FALSE
774 * Searches for vamsas client classes on class path.
776 * @return true if vamsas client is present on classpath
778 public static boolean vamsasJarsPresent()
780 if (vamsasJarsArePresent == UNTESTED)
784 if (jalview.jbgui.GDesktop.class.getClassLoader()
785 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
787 jalview.bin.Cache.log.debug(
788 "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
789 vamsasJarsArePresent = TRUE;
790 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
791 lvclient.setLevel(Level.toLevel(Cache
792 .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
794 lvclient.addAppender(log.getAppender("JalviewLogger"));
795 // Tell the user that debug is enabled
796 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
798 } catch (Exception e)
800 vamsasJarsArePresent = FALSE;
801 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
804 return (vamsasJarsArePresent == TRUE);
808 * internal vamsas class discovery state
810 private static int groovyJarsArePresent = (Platform.isJS() ? FALSE
814 * Searches for vamsas client classes on class path.
816 * @return true if vamsas client is present on classpath
818 public static boolean groovyJarsPresent()
820 if (groovyJarsArePresent == UNTESTED)
824 if (Cache.class.getClassLoader()
825 .loadClass("groovy.lang.GroovyObject") != null)
827 jalview.bin.Cache.log.debug(
828 "Found Groovy (groovy.lang.GroovyObject can be loaded)");
829 groovyJarsArePresent = TRUE;
830 Logger lgclient = Logger.getLogger("groovy");
831 lgclient.setLevel(Level.toLevel(Cache
832 .getDefault("logs.Groovy.Level", Level.INFO.toString())));
834 lgclient.addAppender(log.getAppender("JalviewLogger"));
835 // Tell the user that debug is enabled
836 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
840 groovyJarsArePresent = FALSE;
841 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
842 } catch (Exception e)
844 groovyJarsArePresent = FALSE;
845 jalview.bin.Cache.log.debug("Groovy Classes are not present");
848 return (groovyJarsArePresent == TRUE);
852 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
855 protected static Object tracker = null;
857 protected static Class<?> trackerfocus = null;
859 protected static Class<?> jgoogleanalyticstracker = null;
862 * Initialise the google tracker if it is not done already.
864 public static void initGoogleTracker()
867 // TODO: SwingJS JavaScript tracker?
871 if (jgoogleanalyticstracker == null)
873 // try to get the tracker class
876 jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
877 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
878 trackerfocus = Cache.class.getClassLoader()
879 .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
880 } catch (Exception e)
883 "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
885 jgoogleanalyticstracker = null;
890 // now initialise tracker
891 Exception re = null, ex = null;
893 String vrs = "No Version Accessible";
896 // Google analytics tracking code for Library Finder
897 tracker = jgoogleanalyticstracker
898 .getConstructor(new Class[]
899 { String.class, String.class, String.class })
900 .newInstance(new Object[]
902 (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
903 + getDefault("BUILD_DATE", "unknown")),
905 jgoogleanalyticstracker
906 .getMethod("trackAsynchronously", new Class[]
908 .invoke(tracker, new Object[]
909 { trackerfocus.getConstructor(new Class[] { String.class })
910 .newInstance(new Object[]
911 { "Application Started." }) });
912 } catch (RuntimeException e)
915 } catch (Exception e)
922 if (re != null || ex != null || err != null)
928 log.debug("Caught runtime exception in googletracker init:",
934 "Failed to initialise GoogleTracker for Jalview Desktop with version "
941 "Whilst initing GoogleTracker for Jalview Desktop version "
951 "Debug: Caught runtime exception in googletracker init:"
953 re.printStackTrace();
958 "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
960 ex.printStackTrace();
966 "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
968 err.printStackTrace();
974 log.debug("Successfully initialised tracker.");
980 * get the user's default colour if available
986 public static Color getDefaultColour(String property, Color defcolour)
988 String colprop = getProperty(property);
993 Color col = ColorUtils.parseColourString(colprop);
996 log.warn("Couldn't parse '" + colprop + "' as a colour for "
999 return (col == null) ? defcolour : col;
1003 * store a colour as a Jalview user default property
1008 public static void setColourProperty(String property, Color colour)
1010 setProperty(property, jalview.util.Format.getHexString(colour));
1014 * Stores a formatted date in a jalview property, using a fixed locale.
1016 * @param propertyName
1018 * @return the formatted date string
1020 public static String setDateProperty(String propertyName, Date date)
1022 String formatted = date_format.format(date);
1023 setProperty(propertyName, formatted);
1028 * Reads a date stored in a Jalview property, parses it (using a fixed locale
1029 * format) and returns as a Date, or null if parsing fails
1031 * @param propertyName
1035 public static Date getDateProperty(String propertyName)
1037 String val = getProperty(propertyName);
1042 return date_format.parse(val);
1043 } catch (Exception ex)
1045 System.err.println("Invalid or corrupt date in property '"
1046 + propertyName + "' : value was '" + val + "'");
1053 * get and parse a property as an integer. send any parsing problems to
1057 * @return null or Integer
1059 public static Integer getIntegerProperty(String property)
1061 String val = getProperty(property);
1062 if (val != null && (val = val.trim()).length() > 0)
1066 return Integer.valueOf(val);
1067 } catch (NumberFormatException x)
1069 System.err.println("Invalid integer in property '" + property
1070 + "' (value was '" + val + "')");
1077 * Set the specified value, or remove it if null or empty. Does not save the
1083 public static void setOrRemove(String propName, String value)
1085 if (propName == null)
1089 if (value == null || value.trim().length() < 1)
1091 getInstance().applicationProperties.remove(propName);
1095 getInstance().applicationProperties.setProperty(propName, value);
1100 * Loads in user colour schemes from files.
1103 * a '|'-delimited list of file paths
1105 public static void initUserColourSchemes(String files)
1107 if (files == null || files.length() == 0)
1112 // In case colours can't be loaded, we'll remove them
1113 // from the default list here.
1114 StringBuffer coloursFound = new StringBuffer();
1115 StringTokenizer st = new StringTokenizer(files, "|");
1116 while (st.hasMoreElements())
1118 String file = st.nextToken();
1121 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1124 if (coloursFound.length() > 0)
1126 coloursFound.append("|");
1128 coloursFound.append(file);
1129 ColourSchemes.getInstance().registerColourScheme(ucs);
1131 } catch (Exception ex)
1133 System.out.println("Error loading User ColourFile\n" + ex);
1136 if (!files.equals(coloursFound.toString()))
1138 if (coloursFound.toString().length() > 1)
1140 setProperty(Preferences.USER_DEFINED_COLOURS,
1141 coloursFound.toString());
1145 getInstance().applicationProperties
1146 .remove(Preferences.USER_DEFINED_COLOURS);