2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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.</li>
137 * @version $Revision$
142 * property giving log4j level for CASTOR loggers
144 public static final String CASTORLOGLEVEL = "logs.Castor.level";
147 * property giving log4j level for AXIS loggers
149 public static final String AXISLOGLEVEL = "logs.Axis.level";
152 * property giving log4j level for Jalview Log
154 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
156 public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
158 public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
160 public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
163 * Initialises the Jalview Application Log
165 public static Logger log;
167 /** Jalview Properties */
168 public static Properties applicationProperties = new Properties();
170 /** Default file is ~/.jalview_properties */
171 static String propertiesFile;
173 public static void initLogger()
181 // TODO: redirect stdout and stderr here in order to grab the output of
184 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
186 ap.setName("JalviewLogger");
187 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
189 Logger laxis = Logger.getLogger("org.apache.axis");
190 Logger lcastor = Logger.getLogger("org.exolab.castor");
191 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
193 laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
194 Level.INFO.toString())));
195 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
196 Level.INFO.toString())));
197 lcastor = Logger.getLogger("org.exolab.castor.xml");
198 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
199 Level.INFO.toString())));
200 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
201 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
202 // Level.INFO.toString())));
203 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
204 "logs.Jalview.level", Level.INFO.toString())));
205 // laxis.addAppender(ap);
206 // lcastor.addAppender(ap);
207 // jalview.bin.Cache.log.addAppender(ap);
208 // Tell the user that debug is enabled
209 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
210 } catch (Exception ex)
212 System.err.println("Problems initializing the log4j system\n");
213 ex.printStackTrace(System.err);
217 /** Called when Jalview is started */
218 public static void loadProperties(String propsFile)
220 propertiesFile = propsFile;
221 if (propsFile == null)
223 propertiesFile = System.getProperty("user.home") + File.separatorChar
224 + ".jalview_properties";
229 FileInputStream fis = new FileInputStream(propertiesFile);
230 applicationProperties.load(fis);
231 applicationProperties.remove("LATEST_VERSION");
232 applicationProperties.remove("VERSION");
234 } catch (Exception ex)
236 System.out.println("Error reading properties file: " + ex);
239 if (getDefault("USE_PROXY", false))
241 System.out.println("Using proxyServer: "
242 + getDefault("PROXY_SERVER", null) + " proxyPort: "
243 + getDefault("PROXY_PORT", null));
245 .setProperty("http.proxyHost", getDefault("PROXY_SERVER",
247 System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
250 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
251 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
252 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
255 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
256 .getCodeSource().getLocation().toString().concat(
257 "!/.build_properties"));
259 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
261 InputStream in = localJarFileURL.openStream();
262 applicationProperties.load(in);
264 } catch (Exception ex)
266 System.out.println("Error reading build details: " + ex);
267 applicationProperties.remove("VERSION");
270 String jnlpVersion = System.getProperty("jalview.version");
271 String codeVersion = getProperty("VERSION");
273 if (codeVersion == null)
275 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
276 codeVersion = "Test";
277 jnlpVersion = "Test";
280 System.out.println("Jalview Version: " + codeVersion);
282 // jnlpVersion will be null if we're using InstallAnywhere
283 // Dont do this check if running in headless mode
284 if (jnlpVersion == null
285 && getDefault("VERSION_CHECK", true)
286 && (System.getProperty("java.awt.headless") == null || System
287 .getProperty("java.awt.headless").equals("false")))
290 class VersionChecker extends Thread
294 String orgtimeout = System
295 .getProperty("sun.net.client.defaultConnectTimeout");
296 if (orgtimeout == null)
299 System.out.println("# INFO: Setting default net timeout to "
300 + orgtimeout + " seconds.");
302 String jnlpVersion = null;
305 System.setProperty("sun.net.client.defaultConnectTimeout",
307 java.net.URL url = new java.net.URL(
308 "http://www.jalview.org/webstart/jalview.jnlp");
309 BufferedReader in = new BufferedReader(new InputStreamReader(
312 while ((line = in.readLine()) != null)
314 if (line.indexOf("jalview.version") == -1)
319 line = line.substring(line.indexOf("value=") + 7);
320 line = line.substring(0, line.lastIndexOf("\""));
324 } catch (Exception ex)
327 .println("Non-fatal exceptions when checking version at www.jalview.org :");
328 System.out.println(ex);
329 jnlpVersion = getProperty("VERSION");
331 System.setProperty("sun.net.client.defaultConnectTimeout",
334 setProperty("LATEST_VERSION", jnlpVersion);
338 VersionChecker vc = new VersionChecker();
343 if (jnlpVersion != null)
345 setProperty("LATEST_VERSION", jnlpVersion);
349 applicationProperties.remove("LATEST_VERSION");
353 setProperty("VERSION", codeVersion);
355 // LOAD USERDEFINED COLOURS
356 jalview.gui.UserDefinedColours
357 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
358 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
363 * Gets Jalview application property of given key. Returns null if key not
369 * @return Property value
371 public static String getProperty(String key)
373 return applicationProperties.getProperty(key);
377 * These methods are used when checking if the saved preference is different
378 * to the default setting
381 public static boolean getDefault(String property, boolean def)
383 String string = getProperty(property);
386 def = Boolean.valueOf(string).booleanValue();
393 * These methods are used when checking if the saved preference is different
394 * to the default setting
396 public static String getDefault(String property, String def)
398 String string = getProperty(property);
408 * Stores property in the file "HOME_DIR/.jalview_properties"
413 * String value of property
415 * @return String value of property
417 public static String setProperty(String key, String obj)
421 FileOutputStream out = new FileOutputStream(propertiesFile);
422 applicationProperties.setProperty(key, obj);
423 applicationProperties.store(out, "---JalviewX Properties File---");
425 } catch (Exception ex)
427 System.out.println("Error setting property: " + key + " " + obj
434 * remove the specified property from the jalview properties file
438 public static void removeProperty(String string)
440 applicationProperties.remove(string);
445 * save the properties to the jalview properties path
447 public static void saveProperties()
451 FileOutputStream out = new FileOutputStream(propertiesFile);
452 applicationProperties.store(out, "---JalviewX Properties File---");
454 } catch (Exception ex)
456 System.out.println("Error saving properties: " + ex);
461 * internal vamsas class discovery state
463 private static int vamsasJarsArePresent = -1;
466 * Searches for vamsas client classes on class path.
468 * @return true if vamsas client is present on classpath
470 public static boolean vamsasJarsPresent()
472 if (vamsasJarsArePresent == -1)
476 if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
477 "uk.ac.vamsas.client.VorbaId") != null)
479 jalview.bin.Cache.log
480 .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
481 vamsasJarsArePresent = 1;
482 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
483 lvclient.setLevel(Level.toLevel(Cache.getDefault(
484 "logs.Vamsas.Level", Level.INFO.toString())));
486 lvclient.addAppender(log.getAppender("JalviewLogger"));
487 // Tell the user that debug is enabled
488 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
490 } catch (Exception e)
492 vamsasJarsArePresent = 0;
493 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
496 return (vamsasJarsArePresent > 0);
500 * internal vamsas class discovery state
502 private static int groovyJarsArePresent = -1;
505 * Searches for vamsas client classes on class path.
507 * @return true if vamsas client is present on classpath
509 public static boolean groovyJarsPresent()
511 if (groovyJarsArePresent == -1)
515 if (Cache.class.getClassLoader().loadClass(
516 "groovy.lang.GroovyObject") != null)
518 jalview.bin.Cache.log
519 .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
520 groovyJarsArePresent = 1;
521 Logger lgclient = Logger.getLogger("groovy");
522 lgclient.setLevel(Level.toLevel(Cache.getDefault(
523 "logs.Groovy.Level", Level.INFO.toString())));
525 lgclient.addAppender(log.getAppender("JalviewLogger"));
526 // Tell the user that debug is enabled
527 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
531 groovyJarsArePresent = 0;
532 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
533 } catch (Exception e)
535 groovyJarsArePresent = 0;
536 jalview.bin.Cache.log.debug("Groovy Classes are not present");
539 return (groovyJarsArePresent > 0);
543 * generate Das1Sources from the local das source list
545 * @return Vector of Das1Sources
547 public static Vector getLocalDasSources()
549 Vector localSources = new Vector();
550 String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
553 StringTokenizer st = new StringTokenizer(local, "\t");
554 while (st.hasMoreTokens())
556 String token = st.nextToken();
557 int bar = token.indexOf("|");
558 Das1Source source = new Das1Source();
559 source.setUrl(token.substring(bar + 1));
560 if (source.getUrl().startsWith("sequence:"))
562 source.setUrl(source.getUrl().substring(9));
563 // this source also serves sequences as well as features
564 source.setCapabilities(new String[]
565 { "sequence", "features" });
569 // default is that all user added sources serve features
570 source.setCapabilities(new String[]
574 source.setNickname(token.substring(0, bar));
576 localSources.addElement(source);
583 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
586 protected static Object tracker = null;
588 protected static Class trackerfocus = null;
590 protected static Class jgoogleanalyticstracker = null;
593 * Initialise the google tracker if it is not done already.
595 public static void initGoogleTracker()
599 if (jgoogleanalyticstracker == null)
601 // try to get the tracker class
604 jgoogleanalyticstracker = Cache.class
607 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
608 trackerfocus = Cache.class.getClassLoader().loadClass(
609 "com.boxysystems.jgoogleanalytics.FocusPoint");
610 } catch (Exception e)
613 .debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
615 jgoogleanalyticstracker = null;
620 // now initialise tracker
621 Exception re = null, ex = null;
623 String vrs = "No Version Accessible";
626 // Google analytics tracking code for Library Finder
627 tracker = jgoogleanalyticstracker.getConstructor(new Class[]
628 { String.class, String.class, String.class }).newInstance(
632 (vrs = jalview.bin.Cache.getProperty("VERSION")
634 + jalview.bin.Cache.getDefault("BUILD_DATE",
635 "unknown")), "UA-9060947-1" });
636 jgoogleanalyticstracker.getMethod("trackAsynchronously",
638 { trackerfocus }).invoke(tracker, new Object[]
639 { trackerfocus.getConstructor(new Class[]
640 { String.class }).newInstance(new Object[]
641 { "Application Started." }) });
642 } catch (RuntimeException e)
645 } catch (Exception e)
652 if (re != null || ex != null || err != null)
659 "Caught runtime exception in googletracker init:",
663 "Failed to initialise GoogleTracker for Jalview Desktop with version "
667 "Whilst initing GoogleTracker for Jalview Desktop version "
675 .println("Debug: Caught runtime exception in googletracker init:"
677 re.printStackTrace();
682 .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
684 ex.printStackTrace();
690 .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
692 err.printStackTrace();
698 log.debug("Successfully initialised tracker.");