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
135 * @version $Revision$
140 * property giving log4j level for CASTOR loggers
142 public static final String CASTORLOGLEVEL = "logs.Castor.level";
145 * property giving log4j level for AXIS loggers
147 public static final String AXISLOGLEVEL = "logs.Axis.level";
150 * property giving log4j level for Jalview Log
152 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
154 public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
156 public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
158 public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
161 * Initialises the Jalview Application Log
163 public static Logger log;
165 /** Jalview Properties */
166 public static Properties applicationProperties = new Properties();
168 /** Default file is ~/.jalview_properties */
169 static String propertiesFile;
171 public static void initLogger()
179 // TODO: redirect stdout and stderr here in order to grab the output of
182 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
184 ap.setName("JalviewLogger");
185 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
187 Logger laxis = Logger.getLogger("org.apache.axis");
188 Logger lcastor = Logger.getLogger("org.exolab.castor");
189 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
191 laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
192 Level.INFO.toString())));
193 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
194 Level.INFO.toString())));
195 lcastor = Logger.getLogger("org.exolab.castor.xml");
196 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
197 Level.INFO.toString())));
198 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
199 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
200 // Level.INFO.toString())));
201 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
202 "logs.Jalview.level", Level.INFO.toString())));
203 // laxis.addAppender(ap);
204 // lcastor.addAppender(ap);
205 // jalview.bin.Cache.log.addAppender(ap);
206 // Tell the user that debug is enabled
207 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
208 } catch (Exception ex)
210 System.err.println("Problems initializing the log4j system\n");
211 ex.printStackTrace(System.err);
215 /** Called when Jalview is started */
216 public static void loadProperties(String propsFile)
218 propertiesFile = propsFile;
219 if (propsFile == null)
221 propertiesFile = System.getProperty("user.home") + File.separatorChar
222 + ".jalview_properties";
227 FileInputStream fis = new FileInputStream(propertiesFile);
228 applicationProperties.load(fis);
229 applicationProperties.remove("LATEST_VERSION");
230 applicationProperties.remove("VERSION");
232 } catch (Exception ex)
234 System.out.println("Error reading properties file: " + ex);
237 if (getDefault("USE_PROXY", false))
239 System.out.println("Using proxyServer: "
240 + getDefault("PROXY_SERVER", null) + " proxyPort: "
241 + getDefault("PROXY_PORT", null));
243 .setProperty("http.proxyHost", getDefault("PROXY_SERVER",
245 System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
248 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
249 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
250 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
253 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
254 .getCodeSource().getLocation().toString().concat(
255 "!/.build_properties"));
257 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
259 InputStream in = localJarFileURL.openStream();
260 applicationProperties.load(in);
262 } catch (Exception ex)
264 System.out.println("Error reading build details: " + ex);
265 applicationProperties.remove("VERSION");
268 String jnlpVersion = System.getProperty("jalview.version");
269 String codeVersion = getProperty("VERSION");
271 if (codeVersion == null)
273 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
274 codeVersion = "Test";
275 jnlpVersion = "Test";
278 System.out.println("Jalview Version: " + codeVersion);
280 // jnlpVersion will be null if we're using InstallAnywhere
281 // Dont do this check if running in headless mode
282 if (jnlpVersion == null
283 && getDefault("VERSION_CHECK", true)
284 && (System.getProperty("java.awt.headless") == null || System
285 .getProperty("java.awt.headless").equals("false")))
288 class VersionChecker extends Thread
292 String orgtimeout = System
293 .getProperty("sun.net.client.defaultConnectTimeout");
294 if (orgtimeout == null)
297 System.out.println("# INFO: Setting default net timeout to "
298 + orgtimeout + " seconds.");
300 String jnlpVersion = null;
303 System.setProperty("sun.net.client.defaultConnectTimeout",
305 java.net.URL url = new java.net.URL(
306 "http://www.jalview.org/webstart/jalview.jnlp");
307 BufferedReader in = new BufferedReader(new InputStreamReader(
310 while ((line = in.readLine()) != null)
312 if (line.indexOf("jalview.version") == -1)
317 line = line.substring(line.indexOf("value=") + 7);
318 line = line.substring(0, line.lastIndexOf("\""));
322 } catch (Exception ex)
325 .println("Non-fatal exceptions when checking version at www.jalview.org :");
326 System.out.println(ex);
327 jnlpVersion = getProperty("VERSION");
329 System.setProperty("sun.net.client.defaultConnectTimeout",
332 setProperty("LATEST_VERSION", jnlpVersion);
336 VersionChecker vc = new VersionChecker();
341 if (jnlpVersion != null)
343 setProperty("LATEST_VERSION", jnlpVersion);
347 applicationProperties.remove("LATEST_VERSION");
351 setProperty("VERSION", codeVersion);
353 // LOAD USERDEFINED COLOURS
354 jalview.gui.UserDefinedColours
355 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
356 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
361 * Gets Jalview application property of given key. Returns null if key not
367 * @return Property value
369 public static String getProperty(String key)
371 return applicationProperties.getProperty(key);
375 * These methods are used when checking if the saved preference is different
376 * to the default setting
379 public static boolean getDefault(String property, boolean def)
381 String string = getProperty(property);
384 def = Boolean.valueOf(string).booleanValue();
391 * These methods are used when checking if the saved preference is different
392 * to the default setting
394 public static String getDefault(String property, String def)
396 String string = getProperty(property);
406 * Stores property in the file "HOME_DIR/.jalview_properties"
411 * String value of property
413 * @return String value of property
415 public static String setProperty(String key, String obj)
419 FileOutputStream out = new FileOutputStream(propertiesFile);
420 applicationProperties.setProperty(key, obj);
421 applicationProperties.store(out, "---JalviewX Properties File---");
423 } catch (Exception ex)
425 System.out.println("Error setting property: " + key + " " + obj
432 * remove the specified property from the jalview properties file
436 public static void removeProperty(String string)
438 applicationProperties.remove(string);
443 * save the properties to the jalview properties path
445 public static void saveProperties()
449 FileOutputStream out = new FileOutputStream(propertiesFile);
450 applicationProperties.store(out, "---JalviewX Properties File---");
452 } catch (Exception ex)
454 System.out.println("Error saving properties: " + ex);
459 * internal vamsas class discovery state
461 private static int vamsasJarsArePresent = -1;
464 * Searches for vamsas client classes on class path.
466 * @return true if vamsas client is present on classpath
468 public static boolean vamsasJarsPresent()
470 if (vamsasJarsArePresent == -1)
474 if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
475 "uk.ac.vamsas.client.VorbaId") != null)
477 jalview.bin.Cache.log
478 .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
479 vamsasJarsArePresent = 1;
480 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
481 lvclient.setLevel(Level.toLevel(Cache.getDefault(
482 "logs.Vamsas.Level", Level.INFO.toString())));
484 lvclient.addAppender(log.getAppender("JalviewLogger"));
485 // Tell the user that debug is enabled
486 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
488 } catch (Exception e)
490 vamsasJarsArePresent = 0;
491 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
494 return (vamsasJarsArePresent > 0);
498 * internal vamsas class discovery state
500 private static int groovyJarsArePresent = -1;
503 * Searches for vamsas client classes on class path.
505 * @return true if vamsas client is present on classpath
507 public static boolean groovyJarsPresent()
509 if (groovyJarsArePresent == -1)
513 if (Cache.class.getClassLoader().loadClass(
514 "groovy.lang.GroovyObject") != null)
516 jalview.bin.Cache.log
517 .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
518 groovyJarsArePresent = 1;
519 Logger lgclient = Logger.getLogger("groovy");
520 lgclient.setLevel(Level.toLevel(Cache.getDefault(
521 "logs.Groovy.Level", Level.INFO.toString())));
523 lgclient.addAppender(log.getAppender("JalviewLogger"));
524 // Tell the user that debug is enabled
525 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
529 groovyJarsArePresent = 0;
530 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
531 } catch (Exception e)
533 groovyJarsArePresent = 0;
534 jalview.bin.Cache.log.debug("Groovy Classes are not present");
537 return (groovyJarsArePresent > 0);
541 * generate Das1Sources from the local das source list
543 * @return Vector of Das1Sources
545 public static Vector getLocalDasSources()
547 Vector localSources = new Vector();
548 String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
551 StringTokenizer st = new StringTokenizer(local, "\t");
552 while (st.hasMoreTokens())
554 String token = st.nextToken();
555 int bar = token.indexOf("|");
556 Das1Source source = new Das1Source();
557 source.setUrl(token.substring(bar + 1));
558 if (source.getUrl().startsWith("sequence:"))
560 source.setUrl(source.getUrl().substring(9));
561 // this source also serves sequences as well as features
562 source.setCapabilities(new String[]
563 { "sequence", "features" });
567 // default is that all user added sources serve features
568 source.setCapabilities(new String[]
572 source.setNickname(token.substring(0, bar));
574 localSources.addElement(source);
581 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
584 protected static Object tracker = null;
586 protected static Class trackerfocus = null;
588 protected static Class jgoogleanalyticstracker = null;
591 * Initialise the google tracker if it is not done already.
593 public static void initGoogleTracker()
597 if (jgoogleanalyticstracker == null)
599 // try to get the tracker class
602 jgoogleanalyticstracker = Cache.class
605 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
606 trackerfocus = Cache.class.getClassLoader().loadClass(
607 "com.boxysystems.jgoogleanalytics.FocusPoint");
608 } catch (Exception e)
611 .debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
613 jgoogleanalyticstracker = null;
618 // now initialise tracker
619 Exception re = null, ex = null;
621 String vrs = "No Version Accessible";
624 // Google analytics tracking code for Library Finder
625 tracker = jgoogleanalyticstracker.getConstructor(new Class[]
626 { String.class, String.class, String.class }).newInstance(
630 (vrs = jalview.bin.Cache.getProperty("VERSION")
632 + jalview.bin.Cache.getDefault("BUILD_DATE",
633 "unknown")), "UA-9060947-1" });
634 jgoogleanalyticstracker.getMethod("trackAsynchronously",
636 { trackerfocus }).invoke(tracker, new Object[]
637 { trackerfocus.getConstructor(new Class[]
638 { String.class }).newInstance(new Object[]
639 { "Application Started." }) });
640 } catch (RuntimeException e)
643 } catch (Exception e)
650 if (re != null || ex != null || err != null)
657 "Caught runtime exception in googletracker init:",
661 "Failed to initialise GoogleTracker for Jalview Desktop with version "
665 "Whilst initing GoogleTracker for Jalview Desktop version "
673 .println("Debug: Caught runtime exception in googletracker init:"
675 re.printStackTrace();
680 .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
682 ex.printStackTrace();
688 .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
690 err.printStackTrace();
696 log.debug("Successfully initialised tracker.");