2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
23 import org.apache.log4j.*;
24 import org.biojava.dasobert.dasregistry.Das1Source;
27 * Stores and retrieves Jalview Application Properties Lists and fields within
28 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
29 * are alternative values for a tag. <br>
31 * Current properties include:
34 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
35 * logging level for axis (used for web services) <br>
37 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
38 * the logging level for castor (used for serialization) <br>
40 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
42 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
44 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.</li>
45 * <li>SCREEN_WIDTH</li>
46 * <li>SCREEN_HEIGHT</li>
47 * <li>SCREEN_Y=285</li>
48 * <li>SCREEN_X=371</li>
49 * <li>SHOW_FULLSCREEN boolean</li>
50 * <li>FONT_NAME java font name for alignment text display</li>
51 * <li>FONT_SIZE size of displayed alignment text</li>
52 * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
53 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
54 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
55 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
56 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
57 * <li>SHOW_IDENTITY show percentage identity annotation</li>
58 * <li>SHOW_QUALITY show alignment quality annotation</li>
59 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
60 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
61 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
63 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
64 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
65 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
66 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
67 * <li>VERSION the version of the jalview build</li>
68 * <li>BUILD_DATE date of this build</li>
69 * <li>LATEST_VERSION the latest jalview version advertised on the
70 * www.jalview.org</li>
71 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
73 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
75 * <li>RECENT_URL list of recently retrieved URLs</li>
76 * <li>RECENT_FILE list of recently opened files</li>
77 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
78 * <li>PROXY_SERVER the proxy</li>
80 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
82 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
84 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
85 * collecting usage statistics</li>
86 * <li>DAS_LOCAL_SOURCE list of local das sources</li>
87 * <li>SHOW_OVERVIEW boolean for overview window display</li>
88 * <li>ANTI_ALIAS boolean for smooth fonts</li>
89 * <li>RIGHT_ALIGN_IDS boolean</li>
90 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
91 * <li>PAD_GAPS boolean</li>
92 * <li>ID_ITALICS boolean</li>
93 * <li>SHOW_JV_SUFFIX</li>
94 * <li>WRAP_ALIGNMENT</li>
95 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
97 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
98 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
100 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
101 * jalview.utils.GroupURLLink for more info</li>
102 * <li>DAS_REGISTRY_URL the registry to query</li>
103 * <li>DEFAULT_BROWSER for unix</li>
104 * <li>DAS_ACTIVE_SOURCE list of active sources</li>
105 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
107 * <li>VERSION_CHECK (true) check for the latest release version from
108 * www.jalview.org</li>
109 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
111 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
113 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
114 * displayed as '.'</li>
115 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
116 * order of a newly displayed tree</li>
117 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
118 * sequence ID strings before attempting retrieval from any datasource</li>
119 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
121 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
122 * in the alignment.</li>
123 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
125 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
127 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
128 * respond to selections made in other alignments containing the same sequences.
130 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
131 * warning dialog box is displayed.</li>
140 * @version $Revision$
145 * property giving log4j level for CASTOR loggers
147 public static final String CASTORLOGLEVEL = "logs.Castor.level";
150 * property giving log4j level for AXIS loggers
152 public static final String AXISLOGLEVEL = "logs.Axis.level";
155 * property giving log4j level for Jalview Log
157 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
159 public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
161 public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
163 public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
166 * Initialises the Jalview Application Log
168 public static Logger log;
170 /** Jalview Properties */
171 public static Properties applicationProperties = new Properties();
173 /** Default file is ~/.jalview_properties */
174 static String propertiesFile;
176 private static boolean propsAreReadOnly=false;
178 public static void initLogger()
186 // TODO: redirect stdout and stderr here in order to grab the output of
189 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
191 ap.setName("JalviewLogger");
192 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
194 Logger laxis = Logger.getLogger("org.apache.axis");
195 Logger lcastor = Logger.getLogger("org.exolab.castor");
196 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
198 laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
199 Level.INFO.toString())));
200 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
201 Level.INFO.toString())));
202 lcastor = Logger.getLogger("org.exolab.castor.xml");
203 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
204 Level.INFO.toString())));
205 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
206 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
207 // Level.INFO.toString())));
208 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
209 "logs.Jalview.level", Level.INFO.toString())));
210 // laxis.addAppender(ap);
211 // lcastor.addAppender(ap);
212 // jalview.bin.Cache.log.addAppender(ap);
213 // Tell the user that debug is enabled
214 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
215 } catch (Exception ex)
217 System.err.println("Problems initializing the log4j system\n");
218 ex.printStackTrace(System.err);
222 /** Called when Jalview is started */
223 public static void loadProperties(String propsFile)
225 propertiesFile = propsFile;
226 if (propsFile == null)
228 propertiesFile = System.getProperty("user.home") + File.separatorChar
229 + ".jalview_properties";
237 fis = new java.net.URL(propertiesFile).openStream();
238 System.out.println("Loading jalview properties from : "
241 .println("Disabling Jalview writing to user's local properties file.");
242 propsAreReadOnly = true;
244 } catch (Exception ex)
250 fis = new FileInputStream(propertiesFile);
252 applicationProperties.load(fis);
253 applicationProperties.remove("LATEST_VERSION");
254 applicationProperties.remove("VERSION");
256 } catch (Exception ex)
258 System.out.println("Error reading properties file: " + ex);
261 if (getDefault("USE_PROXY", false))
263 System.out.println("Using proxyServer: "
264 + getDefault("PROXY_SERVER", null) + " proxyPort: "
265 + getDefault("PROXY_PORT", null));
266 System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));
267 System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
270 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
271 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
272 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
275 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
276 .getCodeSource().getLocation().toString()
277 .concat("!/.build_properties"));
279 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
281 InputStream in = localJarFileURL.openStream();
282 applicationProperties.load(in);
284 } catch (Exception ex)
286 System.out.println("Error reading build details: " + ex);
287 applicationProperties.remove("VERSION");
290 String jnlpVersion = System.getProperty("jalview.version");
291 String codeVersion = getProperty("VERSION");
293 if (codeVersion == null)
295 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
296 codeVersion = "Test";
297 jnlpVersion = "Test";
300 System.out.println("Jalview Version: " + codeVersion);
302 // jnlpVersion will be null if we're using InstallAnywhere
303 // Dont do this check if running in headless mode
304 if (jnlpVersion == null
305 && getDefault("VERSION_CHECK", true)
306 && (System.getProperty("java.awt.headless") == null || System
307 .getProperty("java.awt.headless").equals("false")))
310 class VersionChecker extends Thread
314 String orgtimeout = System
315 .getProperty("sun.net.client.defaultConnectTimeout");
316 if (orgtimeout == null)
319 System.out.println("# INFO: Setting default net timeout to "
320 + orgtimeout + " seconds.");
322 String jnlpVersion = null;
325 System.setProperty("sun.net.client.defaultConnectTimeout",
327 java.net.URL url = new java.net.URL(
328 "http://www.jalview.org/webstart/jalview.jnlp");
329 BufferedReader in = new BufferedReader(new InputStreamReader(
332 while ((line = in.readLine()) != null)
334 if (line.indexOf("jalview.version") == -1)
339 line = line.substring(line.indexOf("value=") + 7);
340 line = line.substring(0, line.lastIndexOf("\""));
344 } catch (Exception ex)
347 .println("Non-fatal exceptions when checking version at www.jalview.org :");
348 System.out.println(ex);
349 jnlpVersion = getProperty("VERSION");
351 System.setProperty("sun.net.client.defaultConnectTimeout",
354 setProperty("LATEST_VERSION", jnlpVersion);
358 VersionChecker vc = new VersionChecker();
363 if (jnlpVersion != null)
365 setProperty("LATEST_VERSION", jnlpVersion);
369 applicationProperties.remove("LATEST_VERSION");
373 setProperty("VERSION", codeVersion);
375 // LOAD USERDEFINED COLOURS
376 jalview.gui.UserDefinedColours
377 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
378 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
383 * Gets Jalview application property of given key. Returns null if key not
389 * @return Property value
391 public static String getProperty(String key)
393 return applicationProperties.getProperty(key);
397 * These methods are used when checking if the saved preference is different
398 * to the default setting
401 public static boolean getDefault(String property, boolean def)
403 String string = getProperty(property);
406 def = Boolean.valueOf(string).booleanValue();
413 * These methods are used when checking if the saved preference is different
414 * to the default setting
416 public static String getDefault(String property, String def)
418 String string = getProperty(property);
428 * Stores property in the file "HOME_DIR/.jalview_properties"
433 * String value of property
435 * @return String value of property
437 public static String setProperty(String key, String obj)
442 applicationProperties.setProperty(key, obj);
443 if (!propsAreReadOnly)
445 FileOutputStream out = new FileOutputStream(propertiesFile);
446 applicationProperties.store(out, "---JalviewX Properties File---");
449 } catch (Exception ex)
451 System.out.println("Error setting property: " + key + " " + obj
458 * remove the specified property from the jalview properties file
462 public static void removeProperty(String string)
464 applicationProperties.remove(string);
469 * save the properties to the jalview properties path
471 public static void saveProperties()
473 if (!propsAreReadOnly)
477 FileOutputStream out = new FileOutputStream(propertiesFile);
478 applicationProperties.store(out, "---JalviewX Properties File---");
480 } catch (Exception ex)
482 System.out.println("Error saving properties: " + ex);
488 * internal vamsas class discovery state
490 private static int vamsasJarsArePresent = -1;
493 * Searches for vamsas client classes on class path.
495 * @return true if vamsas client is present on classpath
497 public static boolean vamsasJarsPresent()
499 if (vamsasJarsArePresent == -1)
503 if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
504 "uk.ac.vamsas.client.VorbaId") != null)
506 jalview.bin.Cache.log
507 .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
508 vamsasJarsArePresent = 1;
509 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
510 lvclient.setLevel(Level.toLevel(Cache.getDefault(
511 "logs.Vamsas.Level", Level.INFO.toString())));
513 lvclient.addAppender(log.getAppender("JalviewLogger"));
514 // Tell the user that debug is enabled
515 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
517 } catch (Exception e)
519 vamsasJarsArePresent = 0;
520 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
523 return (vamsasJarsArePresent > 0);
527 * internal vamsas class discovery state
529 private static int groovyJarsArePresent = -1;
532 * Searches for vamsas client classes on class path.
534 * @return true if vamsas client is present on classpath
536 public static boolean groovyJarsPresent()
538 if (groovyJarsArePresent == -1)
542 if (Cache.class.getClassLoader().loadClass(
543 "groovy.lang.GroovyObject") != null)
545 jalview.bin.Cache.log
546 .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
547 groovyJarsArePresent = 1;
548 Logger lgclient = Logger.getLogger("groovy");
549 lgclient.setLevel(Level.toLevel(Cache.getDefault(
550 "logs.Groovy.Level", Level.INFO.toString())));
552 lgclient.addAppender(log.getAppender("JalviewLogger"));
553 // Tell the user that debug is enabled
554 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
558 groovyJarsArePresent = 0;
559 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
560 } catch (Exception e)
562 groovyJarsArePresent = 0;
563 jalview.bin.Cache.log.debug("Groovy Classes are not present");
566 return (groovyJarsArePresent > 0);
570 * generate Das1Sources from the local das source list
572 * @return Vector of Das1Sources
574 public static Vector getLocalDasSources()
576 Vector localSources = new Vector();
577 String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
580 StringTokenizer st = new StringTokenizer(local, "\t");
581 while (st.hasMoreTokens())
583 String token = st.nextToken();
584 int bar = token.indexOf("|");
585 Das1Source source = new Das1Source();
586 source.setUrl(token.substring(bar + 1));
587 if (source.getUrl().startsWith("sequence:"))
589 source.setUrl(source.getUrl().substring(9));
590 // this source also serves sequences as well as features
591 source.setCapabilities(new String[]
592 { "sequence", "features" });
596 // default is that all user added sources serve features
597 source.setCapabilities(new String[]
601 source.setNickname(token.substring(0, bar));
603 localSources.addElement(source);
610 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
613 protected static Object tracker = null;
615 protected static Class trackerfocus = null;
617 protected static Class jgoogleanalyticstracker = null;
620 * Initialise the google tracker if it is not done already.
622 public static void initGoogleTracker()
626 if (jgoogleanalyticstracker == null)
628 // try to get the tracker class
631 jgoogleanalyticstracker = Cache.class
634 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
635 trackerfocus = Cache.class.getClassLoader().loadClass(
636 "com.boxysystems.jgoogleanalytics.FocusPoint");
637 } catch (Exception e)
639 log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
641 jgoogleanalyticstracker = null;
646 // now initialise tracker
647 Exception re = null, ex = null;
649 String vrs = "No Version Accessible";
652 // Google analytics tracking code for Library Finder
653 tracker = jgoogleanalyticstracker.getConstructor(new Class[]
654 { String.class, String.class, String.class }).newInstance(
658 (vrs = jalview.bin.Cache.getProperty("VERSION")
660 + jalview.bin.Cache.getDefault("BUILD_DATE",
661 "unknown")), "UA-9060947-1" });
662 jgoogleanalyticstracker.getMethod("trackAsynchronously",
664 { trackerfocus }).invoke(tracker, new Object[]
665 { trackerfocus.getConstructor(new Class[]
666 { String.class }).newInstance(new Object[]
667 { "Application Started." }) });
668 } catch (RuntimeException e)
671 } catch (Exception e)
678 if (re != null || ex != null || err != null)
683 log.debug("Caught runtime exception in googletracker init:", re);
686 "Failed to initialise GoogleTracker for Jalview Desktop with version "
690 "Whilst initing GoogleTracker for Jalview Desktop version "
698 .println("Debug: Caught runtime exception in googletracker init:"
700 re.printStackTrace();
705 .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
707 ex.printStackTrace();
713 .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
715 err.printStackTrace();
721 log.debug("Successfully initialised tracker.");