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.ws.sifts.SiftsSettings;
33 import java.awt.Color;
34 import java.io.BufferedReader;
36 import java.io.FileInputStream;
37 import java.io.FileOutputStream;
38 import java.io.InputStream;
39 import java.io.InputStreamReader;
40 import java.text.DateFormat;
41 import java.text.SimpleDateFormat;
42 import java.util.Collections;
43 import java.util.Date;
44 import java.util.Enumeration;
45 import java.util.Locale;
46 import java.util.Properties;
47 import java.util.StringTokenizer;
48 import java.util.TreeSet;
50 import org.apache.log4j.ConsoleAppender;
51 import org.apache.log4j.Level;
52 import org.apache.log4j.Logger;
53 import org.apache.log4j.SimpleLayout;
56 * Stores and retrieves Jalview Application Properties Lists and fields within
57 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
58 * are alternative values for a tag. <br>
60 * Current properties include:
63 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
64 * logging level for axis (used for web services) <br>
66 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
67 * the logging level for castor (used for serialization) <br>
69 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
71 * <li>SCREEN_WIDTH</li>
72 * <li>SCREEN_HEIGHT</li>
73 * <li>SCREEN_Y=285</li>
74 * <li>SCREEN_X=371</li>
75 * <li>SHOW_FULLSCREEN boolean</li>
76 * <li>FONT_NAME java font name for alignment text display</li>
77 * <li>FONT_SIZE size of displayed alignment text</li>
78 * <li>FONT_STYLE style of font displayed (sequence labels are always
80 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
81 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
82 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
83 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
84 * <li>SHOW_IDENTITY show percentage identity annotation</li>
85 * <li>SHOW_QUALITY show alignment quality annotation</li>
86 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
87 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
88 * <li>SORT_ANNOTATIONS currently either SEQUENCE_AND_LABEL or
89 * LABEL_AND_SEQUENCE</li>
90 * <li>SHOW_AUTOCALC_ABOVE true to show autocalculated annotations above
91 * sequence annotations</li>
92 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
94 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
95 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
96 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
97 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
98 * <li>VERSION the version of the jalview build</li>
99 * <li>BUILD_DATE date of this build</li>
100 * <li>LATEST_VERSION the latest jalview version advertised on the
101 * www.jalview.org</li>
102 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
104 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
105 * suffix to file</li>
106 * <li>RECENT_URL list of recently retrieved URLs</li>
107 * <li>RECENT_FILE list of recently opened files</li>
108 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
109 * <li>PROXY_SERVER the proxy</li>
110 * <li>PROXY_PORT</li>
111 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
113 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
115 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
116 * collecting usage statistics</li>
117 * <li>DAS_LOCAL_SOURCE list of local das sources</li>
118 * <li>SHOW_OVERVIEW boolean for overview window display</li>
119 * <li>ANTI_ALIAS boolean for smooth fonts</li>
120 * <li>RIGHT_ALIGN_IDS boolean</li>
121 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
122 * <li>PAD_GAPS boolean</li>
123 * <li>ID_ITALICS boolean</li>
124 * <li>SHOW_JV_SUFFIX</li>
125 * <li>WRAP_ALIGNMENT</li>
126 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
128 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
129 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
131 * <li>STORED_LINKS list of name|url pairs which user has entered but are not
133 * <li>DEFAULT_LINK name of single url to be used when user double clicks a
134 * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS)
135 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
136 * jalview.utils.GroupURLLink for more info</li>
137 * <li>DAS_REGISTRY_URL the registry to query</li>
138 * <li>DEFAULT_BROWSER for unix</li>
139 * <li>DAS_ACTIVE_SOURCE list of active sources</li>
140 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
142 * <li>VERSION_CHECK (true) check for the latest release version from
143 * www.jalview.org (or the alias given by the www.jalview.org property)</li>
144 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
146 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
148 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
149 * displayed as '.'</li>
150 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
151 * order of a newly displayed tree</li>
152 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
153 * sequence ID strings before attempting retrieval from any datasource</li>
154 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
156 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
157 * in the alignment.</li>
158 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
160 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
162 * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
163 * logo normalised to row height rather than histogram height.</li>
164 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
165 * respond to selections made in other alignments containing the same sequences.
167 * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
168 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
169 * warning dialog box is displayed.</li>
170 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
171 * when shading by annotation</li>
172 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
173 * when shading by annotation</li>
174 * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
175 * requests to be redirected to a mirror of http://www.jalview.org</li>
176 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
177 * alignment figure to accommodate even the longest sequence ID or annotation
179 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
180 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
181 * will override this).</li>
182 * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
184 * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
185 * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
187 * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
189 * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
191 * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
192 * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
196 * Deprecated settings:
199 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
200 * startup (JWS1 services only)</li>
201 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
202 * (JWS1 services only)</li>
203 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
204 * services in the desktop GUI</li>
205 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
206 * panel in web service preferences</li>
210 * @version $Revision$
215 * property giving log4j level for CASTOR loggers
217 public static final String CASTORLOGLEVEL = "logs.Castor.level";
220 * property giving log4j level for AXIS loggers
222 public static final String AXISLOGLEVEL = "logs.Axis.level";
225 * property giving log4j level for Jalview Log
227 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
229 public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
231 public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
233 public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
238 public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
239 .getProperty("user.home") + File.separatorChar
240 + ".sifts_downloads" + File.separatorChar;
242 private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
244 private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
247 * Identifiers.org download settings
249 private static final String ID_ORG_FILE = System.getProperty("user.home")
250 + File.separatorChar + ".identifiers.org.ids.json";
253 * Allowed values are PDB or mmCIF
255 private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF
258 private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
262 * a date formatter using a fixed (rather than the user's) locale;
263 * this ensures that date properties can be written and re-read successfully
264 * even if the user changes their locale setting
266 private static final DateFormat date_format = SimpleDateFormat
267 .getDateTimeInstance(SimpleDateFormat.MEDIUM,
268 SimpleDateFormat.MEDIUM, Locale.UK);
271 * Initialises the Jalview Application Log
273 public static Logger log;
275 /** Jalview Properties */
276 public static Properties applicationProperties = new Properties()
278 // override results in properties output in alphabetical order
280 public synchronized Enumeration<Object> keys()
282 return Collections.enumeration(new TreeSet<>(super.keySet()));
286 /** Default file is ~/.jalview_properties */
287 static String propertiesFile;
289 private static boolean propsAreReadOnly = /** @j2sNative true || */
292 public static void initLogger()
300 // TODO: redirect stdout and stderr here in order to grab the output of
303 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
305 ap.setName("JalviewLogger");
306 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
308 Logger laxis = Logger.getLogger("org.apache.axis");
309 Logger lcastor = Logger.getLogger("org.exolab.castor");
310 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
312 laxis.setLevel(Level.toLevel(
313 Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
314 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
315 Level.INFO.toString())));
316 lcastor = Logger.getLogger("org.exolab.castor.xml");
317 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
318 Level.INFO.toString())));
319 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
320 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
321 // Level.INFO.toString())));
322 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
323 .getDefault("logs.Jalview.level", Level.INFO.toString())));
324 // laxis.addAppender(ap);
325 // lcastor.addAppender(ap);
326 // jalview.bin.Cache.log.addAppender(ap);
327 // Tell the user that debug is enabled
328 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
329 } catch (Exception ex)
331 System.err.println("Problems initializing the log4j system\n");
332 ex.printStackTrace(System.err);
337 * Loads properties from the given properties file. Any existing properties
340 public static void loadProperties(String propsFile)
342 propertiesFile = propsFile;
343 if (propsFile == null)
345 propertiesFile = System.getProperty("user.home") + File.separatorChar
346 + ".jalview_properties";
350 // don't corrupt the file we've been given.
351 propsAreReadOnly = true;
359 fis = new java.net.URL(propertiesFile).openStream();
361 "Loading jalview properties from : " + propertiesFile);
363 "Disabling Jalview writing to user's local properties file.");
364 propsAreReadOnly = true;
366 } catch (Exception ex)
372 fis = new FileInputStream(propertiesFile);
374 applicationProperties.clear();
375 applicationProperties.load(fis);
377 // remove any old build properties
379 deleteBuildProperties();
381 } catch (Exception ex)
383 System.out.println("Error reading properties file: " + ex);
386 if (getDefault("USE_PROXY", false))
388 String proxyServer = getDefault("PROXY_SERVER", ""),
389 proxyPort = getDefault("PROXY_PORT", "8080");
391 System.out.println("Using proxyServer: " + proxyServer
392 + " proxyPort: " + proxyPort);
394 System.setProperty("http.proxyHost", proxyServer);
395 System.setProperty("http.proxyPort", proxyPort);
398 // LOAD THE AUTHORS FROM THE authors.props file
401 String authorDetails = /** @j2sNative "xxx" || */
403 .concat(Cache.class.getProtectionDomain().getCodeSource()
404 .getLocation().toString().concat("!/authors.props"));
406 java.net.URL localJarFileURL = new java.net.URL(authorDetails);
408 InputStream in = localJarFileURL.openStream();
409 applicationProperties.load(in);
411 } catch (Exception ex)
413 System.out.println("Error reading author details: " + ex);
414 applicationProperties.remove("AUTHORS");
415 applicationProperties.remove("AUTHORFNAMES");
416 applicationProperties.remove("YEAR");
419 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
420 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
421 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
424 String buildDetails = /** @j2sNative "xxx" || */
425 "jar:".concat(Cache.class.getProtectionDomain()
426 .getCodeSource().getLocation().toString()
427 .concat("!/.build_properties"));
429 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
431 InputStream in = localJarFileURL.openStream();
432 applicationProperties.load(in);
434 } catch (Exception ex)
436 System.out.println("Error reading build details: " + ex);
437 applicationProperties.remove("VERSION");
440 String jnlpVersion = System.getProperty("jalview.version");
441 String codeVersion = getProperty("VERSION");
442 String codeInstallation = getProperty("INSTALLATION");
443 if (codeVersion == null)
445 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
446 codeVersion = "Test";
447 jnlpVersion = "Test";
448 codeInstallation = "";
452 codeInstallation = " (" + codeInstallation + ")";
454 new BuildDetails(codeVersion, null, codeInstallation);
457 .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
459 SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
460 .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
462 SiftsSettings.setFailSafePIDThreshold(
463 jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold",
464 DEFAULT_FAIL_SAFE_PID_THRESHOLD));
466 SiftsSettings.setCacheThresholdInDays(
467 jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
468 DEFAULT_CACHE_THRESHOLD_IN_DAYS));
470 IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
471 "http://www.jalview.org/services/identifiers"));
472 IdOrgSettings.setDownloadLocation(ID_ORG_FILE);
475 .println("Jalview Version: " + codeVersion + codeInstallation);
477 StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
478 .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
479 StructureImportSettings
480 .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
481 // StructureImportSettings
482 // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
483 // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
484 // jnlpVersion will be null if we're using InstallAnywhere
485 // Dont do this check if running in headless mode
486 if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
487 && (System.getProperty("java.awt.headless") == null || System
488 .getProperty("java.awt.headless").equals("false")))
491 class VersionChecker extends Thread
496 String orgtimeout = System
497 .getProperty("sun.net.client.defaultConnectTimeout");
498 if (orgtimeout == null)
501 System.out.println("# INFO: Setting default net timeout to "
502 + orgtimeout + " seconds.");
504 String remoteVersion = null;
507 System.setProperty("sun.net.client.defaultConnectTimeout",
509 java.net.URL url = new java.net.URL(Cache
510 .getDefault("www.jalview.org", "http://www.jalview.org")
511 + "/webstart/jalview.jnlp");
512 BufferedReader in = new BufferedReader(
513 new InputStreamReader(url.openStream()));
515 while ((line = in.readLine()) != null)
517 if (line.indexOf("jalview.version") == -1)
522 line = line.substring(line.indexOf("value=") + 7);
523 line = line.substring(0, line.lastIndexOf("\""));
524 remoteVersion = line;
527 } catch (Exception ex)
530 "Non-fatal exception when checking version at www.jalview.org :");
531 System.out.println(ex);
532 remoteVersion = getProperty("VERSION");
534 System.setProperty("sun.net.client.defaultConnectTimeout",
537 setProperty("LATEST_VERSION", remoteVersion);
541 VersionChecker vc = new VersionChecker();
546 if (jnlpVersion != null)
548 setProperty("LATEST_VERSION", jnlpVersion);
552 applicationProperties.remove("LATEST_VERSION");
556 setProperty("VERSION", codeVersion);
558 // LOAD USERDEFINED COLOURS
560 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
561 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
565 private static void deleteBuildProperties()
567 applicationProperties.remove("LATEST_VERSION");
568 applicationProperties.remove("VERSION");
569 applicationProperties.remove("AUTHORS");
570 applicationProperties.remove("AUTHORFNAMES");
571 applicationProperties.remove("YEAR");
572 applicationProperties.remove("BUILD_DATE");
573 applicationProperties.remove("INSTALLATION");
577 * Gets Jalview application property of given key. Returns null if key not
583 * @return Property value
585 public static String getProperty(String key)
587 return applicationProperties.getProperty(key);
591 * These methods are used when checking if the saved preference is different
592 * to the default setting
595 public static boolean getDefault(String property, boolean def)
597 String string = getProperty(property);
600 def = Boolean.valueOf(string).booleanValue();
607 * Answers the value of the given property, or the supplied default value if
608 * the property is not set
610 public static String getDefault(String property, String def)
612 String value = getProperty(property);
613 return value == null ? def : value;
617 * Stores property in the file "HOME_DIR/.jalview_properties"
622 * String value of property
624 * @return previous value of property (or null)
626 public static Object setProperty(String key, String obj)
628 Object oldValue = null;
631 oldValue = applicationProperties.setProperty(key, obj);
632 if (!propsAreReadOnly)
634 FileOutputStream out = new FileOutputStream(propertiesFile);
635 applicationProperties.store(out, "---JalviewX Properties File---");
638 } catch (Exception ex)
641 "Error setting property: " + key + " " + obj + "\n" + ex);
647 * remove the specified property from the jalview properties file
651 public static void removeProperty(String string)
653 applicationProperties.remove(string);
658 * save the properties to the jalview properties path
660 public static void saveProperties()
662 if (!propsAreReadOnly)
666 FileOutputStream out = new FileOutputStream(propertiesFile);
667 applicationProperties.store(out, "---JalviewX Properties File---");
669 } catch (Exception ex)
671 System.out.println("Error saving properties: " + ex);
677 * internal vamsas class discovery state
679 private static int vamsasJarsArePresent = -1;
682 * Searches for vamsas client classes on class path.
684 * @return true if vamsas client is present on classpath
686 public static boolean vamsasJarsPresent()
688 if (vamsasJarsArePresent == -1)
692 if (jalview.jbgui.GDesktop.class.getClassLoader()
693 .loadClass("uk.ac.vamsas.client.VorbaId") != null)
695 jalview.bin.Cache.log.debug(
696 "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
697 vamsasJarsArePresent = 1;
698 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
699 lvclient.setLevel(Level.toLevel(Cache
700 .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
702 lvclient.addAppender(log.getAppender("JalviewLogger"));
703 // Tell the user that debug is enabled
704 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
706 } catch (Exception e)
708 vamsasJarsArePresent = 0;
709 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
712 return (vamsasJarsArePresent > 0);
716 * internal vamsas class discovery state
718 private static int groovyJarsArePresent = -1;
721 * Searches for vamsas client classes on class path.
723 * @return true if vamsas client is present on classpath
725 public static boolean groovyJarsPresent()
727 if (groovyJarsArePresent == -1)
731 if (Cache.class.getClassLoader()
732 .loadClass("groovy.lang.GroovyObject") != null)
734 jalview.bin.Cache.log.debug(
735 "Found Groovy (groovy.lang.GroovyObject can be loaded)");
736 groovyJarsArePresent = 1;
737 Logger lgclient = Logger.getLogger("groovy");
738 lgclient.setLevel(Level.toLevel(Cache
739 .getDefault("logs.Groovy.Level", Level.INFO.toString())));
741 lgclient.addAppender(log.getAppender("JalviewLogger"));
742 // Tell the user that debug is enabled
743 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
747 groovyJarsArePresent = 0;
748 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
749 } catch (Exception e)
751 groovyJarsArePresent = 0;
752 jalview.bin.Cache.log.debug("Groovy Classes are not present");
755 return (groovyJarsArePresent > 0);
759 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
762 protected static Object tracker = null;
764 protected static Class trackerfocus = null;
766 protected static Class jgoogleanalyticstracker = null;
769 * Initialise the google tracker if it is not done already.
771 public static void initGoogleTracker()
775 if (jgoogleanalyticstracker == null)
777 // try to get the tracker class
780 jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
781 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
782 trackerfocus = Cache.class.getClassLoader()
783 .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
784 } catch (Exception e)
787 "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
789 jgoogleanalyticstracker = null;
794 // now initialise tracker
795 Exception re = null, ex = null;
797 String vrs = "No Version Accessible";
800 // Google analytics tracking code for Library Finder
801 tracker = jgoogleanalyticstracker
802 .getConstructor(new Class[]
803 { String.class, String.class, String.class })
804 .newInstance(new Object[]
806 (vrs = jalview.bin.Cache.getProperty("VERSION") + "_"
807 + jalview.bin.Cache.getDefault("BUILD_DATE",
810 jgoogleanalyticstracker
811 .getMethod("trackAsynchronously", new Class[]
813 .invoke(tracker, new Object[]
814 { trackerfocus.getConstructor(new Class[] { String.class })
815 .newInstance(new Object[]
816 { "Application Started." }) });
817 } catch (RuntimeException e)
820 } catch (Exception e)
827 if (re != null || ex != null || err != null)
833 log.debug("Caught runtime exception in googletracker init:",
839 "Failed to initialise GoogleTracker for Jalview Desktop with version "
846 "Whilst initing GoogleTracker for Jalview Desktop version "
856 "Debug: Caught runtime exception in googletracker init:"
858 re.printStackTrace();
863 "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
865 ex.printStackTrace();
871 "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
873 err.printStackTrace();
879 log.debug("Successfully initialised tracker.");
885 * get the user's default colour if available
891 public static Color getDefaultColour(String property, Color defcolour)
893 String colprop = getProperty(property);
898 Color col = ColorUtils.parseColourString(colprop);
901 log.warn("Couldn't parse '" + colprop + "' as a colour for "
904 return (col == null) ? defcolour : col;
908 * store a colour as a Jalview user default property
913 public static void setColourProperty(String property, Color colour)
915 setProperty(property, jalview.util.Format.getHexString(colour));
919 * Stores a formatted date in a jalview property, using a fixed locale.
921 * @param propertyName
923 * @return the formatted date string
925 public static String setDateProperty(String propertyName, Date date)
927 String formatted = date_format.format(date);
928 setProperty(propertyName, formatted);
933 * Reads a date stored in a Jalview property, parses it (using a fixed locale
934 * format) and returns as a Date, or null if parsing fails
936 * @param propertyName
940 public static Date getDateProperty(String propertyName)
942 String val = getProperty(propertyName);
947 return date_format.parse(val);
948 } catch (Exception ex)
950 System.err.println("Invalid or corrupt date in property '"
951 + propertyName + "' : value was '" + val + "'");
958 * get and parse a property as an integer. send any parsing problems to
962 * @return null or Integer
964 public static Integer getIntegerProperty(String property)
966 String val = getProperty(property);
967 if (val != null && (val = val.trim()).length() > 0)
971 return Integer.valueOf(val);
972 } catch (NumberFormatException x)
974 System.err.println("Invalid integer in property '" + property
975 + "' (value was '" + val + "')");
982 * Set the specified value, or remove it if null or empty. Does not save the
988 public static void setOrRemove(String propName, String value)
990 if (propName == null)
994 if (value == null || value.trim().length() < 1)
996 Cache.applicationProperties.remove(propName);
1000 Cache.applicationProperties.setProperty(propName, value);
1005 * Loads in user colour schemes from files.
1008 * a '|'-delimited list of file paths
1010 public static void initUserColourSchemes(String files)
1012 if (files == null || files.length() == 0)
1017 // In case colours can't be loaded, we'll remove them
1018 // from the default list here.
1019 StringBuffer coloursFound = new StringBuffer();
1020 StringTokenizer st = new StringTokenizer(files, "|");
1021 while (st.hasMoreElements())
1023 String file = st.nextToken();
1026 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
1029 if (coloursFound.length() > 0)
1031 coloursFound.append("|");
1033 coloursFound.append(file);
1034 ColourSchemes.getInstance().registerColourScheme(ucs);
1036 } catch (Exception ex)
1038 System.out.println("Error loading User ColourFile\n" + ex);
1041 if (!files.equals(coloursFound.toString()))
1043 if (coloursFound.toString().length() > 1)
1045 setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
1046 coloursFound.toString());
1050 applicationProperties
1051 .remove(UserDefinedColours.USER_DEFINED_COLOURS);
1057 * Add a known domain that implements access-control-allow-origin:* bh 2018
1059 * @param defaultUniprotDomain
1061 public static void addJ2SDirectDatabaseCall(String domain)
1067 * J2S.addDirectDatabaseCall(domain);