2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 import org.apache.log4j.*;
25 import org.biojava.dasobert.dasregistry.Das1Source;
27 import com.boxysystems.jgoogleanalytics.FocusPoint;
28 import com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker;
31 * Stores and retrieves Jalview Application Properties Lists and fields within
32 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
33 * are alternative values for a tag. <br>
35 * Current properties include:
38 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
39 * logging level for axis (used for web services) <br>
41 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
42 * the logging level for castor (used for serialization) <br>
44 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
46 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried
48 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
50 * <li>SCREEN_WIDTH </li>
51 * <li>SCREEN_HEIGHT </li>
52 * <li>SCREEN_Y=285 </li>
53 * <li>SCREEN_X=371 </li>
54 * <li>SHOW_FULLSCREEN boolean </li>
55 * <li>FONT_NAME java font name for alignment text display </li>
56 * <li>FONT_SIZE size of displayed alignment text </li>
57 * <li>FONT_STYLE style of font displayed (sequence labels are always italic)
59 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ') </li>
60 * <li>LAST_DIRECTORY last directory for browsing alignment </li>
61 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files </li>
62 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended </li>
63 * <li>SHOW_IDENTITY show percentage identity annotation </li>
64 * <li>SHOW_QUALITY show alignment quality annotation </li>
65 * <li>SHOW_ANNOTATIONS show alignment annotation rows </li>
66 * <li>SHOW_CONSERVATION show alignment conservation annotation </li>
67 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
68 * annotation row </li>
69 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment </li>
70 * <li>DEFAULT_FILE_FORMAT file format used to save </li>
71 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url) </li>
72 * <li>SHOW_STARTUP_FILE flag to control loading of startup file </li>
73 * <li>VERSION the version of the jalview build </li>
74 * <li>BUILD_DATE date of this build </li>
75 * <li>LATEST_VERSION the latest jalview version advertised on the
76 * www.jalview.org </li>
77 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
79 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
80 * suffix to file </li>
81 * <li>RECENT_URL list of recently retrieved URLs </li>
82 * <li>RECENT_FILE list of recently opened files </li>
83 * <li>USE_PROXY flag for whether a http proxy is to be used </li>
84 * <li>PROXY_SERVER the proxy </li>
85 * <li>PROXY_PORT </li>
86 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
88 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
90 * <li>USAGESTATS (true) Enable google analytics tracker for collecting usage statistics</li>
91 * <li>DAS_LOCAL_SOURCE list of local das sources </li>
92 * <li>SHOW_OVERVIEW boolean for overview window display </li>
93 * <li>ANTI_ALIAS boolean for smooth fonts </li>
94 * <li>RIGHT_ALIGN_IDS boolean </li>
95 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus
97 * <li>PAD_GAPS boolean </li>
98 * <li>ID_ITALICS boolean </li>
99 * <li>SHOW_JV_SUFFIX </li>
100 * <li>WRAP_ALIGNMENT </li>
101 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
103 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity) </li>
104 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
105 * $SEQUENCE_ID$ </li>
106 * <li>DAS_REGISTRY_URL the registry to query </li>
107 * <li>DEFAULT_BROWSER for unix </li>
108 * <li>DAS_ACTIVE_SOURCE list of active sources </li>
109 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
111 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence ID tooltip</li>
112 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence ID tooltip</li>
113 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved displayed as '.'</li>
114 * <li>SORT_BY_TREE (false) sort the current alignment view according to the order of a newly displayed tree</li>
121 * @version $Revision$
126 * property giving log4j level for CASTOR loggers
128 public static final String CASTORLOGLEVEL = "logs.Castor.level";
131 * property giving log4j level for AXIS loggers
133 public static final String AXISLOGLEVEL = "logs.Axis.level";
136 * property giving log4j level for Jalview Log
138 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
140 public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
142 public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
144 public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
147 * Initialises the Jalview Application Log
149 public static Logger log;
151 /** Jalview Properties */
152 public static Properties applicationProperties = new Properties();
154 /** Default file is ~/.jalview_properties */
155 static String propertiesFile;
157 public static void initLogger()
161 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
163 ap.setName("JalviewLogger");
164 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
166 Logger laxis = Logger.getLogger("org.apache.axis");
167 Logger lcastor = Logger.getLogger("org.exolab.castor");
168 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
170 laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
171 Level.INFO.toString())));
172 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
173 Level.INFO.toString())));
174 lcastor = Logger.getLogger("org.exolab.castor.xml");
175 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
176 Level.INFO.toString())));
177 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
178 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
179 // Level.INFO.toString())));
180 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
181 "logs.Jalview.level", Level.INFO.toString())));
182 // laxis.addAppender(ap);
183 // lcastor.addAppender(ap);
184 // jalview.bin.Cache.log.addAppender(ap);
185 // Tell the user that debug is enabled
186 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
187 } catch (Exception ex)
189 System.err.println("Problems initializing the log4j system\n");
190 ex.printStackTrace(System.err);
194 /** Called when Jalview is started */
195 public static void loadProperties(String propsFile)
197 propertiesFile = propsFile;
198 if (propsFile == null)
200 propertiesFile = System.getProperty("user.home") + File.separatorChar
201 + ".jalview_properties";
206 FileInputStream fis = new FileInputStream(propertiesFile);
207 applicationProperties.load(fis);
208 applicationProperties.remove("LATEST_VERSION");
209 applicationProperties.remove("VERSION");
211 } catch (Exception ex)
213 System.out.println("Error reading properties file: " + ex);
216 if (getDefault("USE_PROXY", false))
218 System.out.println("Using proxyServer: "
219 + getDefault("PROXY_SERVER", null) + " proxyPort: "
220 + getDefault("PROXY_PORT", null));
222 .setProperty("http.proxyHost", getDefault("PROXY_SERVER",
224 System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
227 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
228 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
229 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
232 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
233 .getCodeSource().getLocation().toString().concat(
234 "!/.build_properties"));
236 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
238 InputStream in = localJarFileURL.openStream();
239 applicationProperties.load(in);
241 } catch (Exception ex)
243 System.out.println("Error reading build details: " + ex);
244 applicationProperties.remove("VERSION");
247 String jnlpVersion = System.getProperty("jalview.version");
248 String codeVersion = getProperty("VERSION");
250 if (codeVersion == null)
252 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
253 codeVersion = "Test";
254 jnlpVersion = "Test";
257 System.out.println("Jalview Version: " + codeVersion);
259 // jnlpVersion will be null if we're using InstallAnywhere
260 // Dont do this check if running in headless mode
261 if (jnlpVersion == null
262 && (System.getProperty("java.awt.headless") == null || System
263 .getProperty("java.awt.headless").equals("false")))
266 class VersionChecker extends Thread
270 String orgtimeout = System
271 .getProperty("sun.net.client.defaultConnectTimeout");
272 if (orgtimeout == null)
275 System.out.println("# INFO: Setting default net timeout to "
276 + orgtimeout + " seconds.");
278 String jnlpVersion = null;
281 System.setProperty("sun.net.client.defaultConnectTimeout",
283 java.net.URL url = new java.net.URL(
284 "http://www.jalview.org/webstart/jalview.jnlp");
285 BufferedReader in = new BufferedReader(new InputStreamReader(
288 while ((line = in.readLine()) != null)
290 if (line.indexOf("jalview.version") == -1)
295 line = line.substring(line.indexOf("value=") + 7);
296 line = line.substring(0, line.lastIndexOf("\""));
300 } catch (Exception ex)
303 .println("Non-fatal exceptions when checking version at www.jalview.org :");
304 System.out.println(ex);
305 jnlpVersion = getProperty("VERSION");
307 System.setProperty("sun.net.client.defaultConnectTimeout",
310 setProperty("LATEST_VERSION", jnlpVersion);
314 VersionChecker vc = new VersionChecker();
319 if (jnlpVersion != null)
321 setProperty("LATEST_VERSION", jnlpVersion);
325 applicationProperties.remove("LATEST_VERSION");
329 setProperty("VERSION", codeVersion);
331 // LOAD USERDEFINED COLOURS
332 jalview.gui.UserDefinedColours
333 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
334 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
339 * Gets Jalview application property of given key. Returns null if key not
345 * @return Property value
347 public static String getProperty(String key)
349 return applicationProperties.getProperty(key);
353 * These methods are used when checking if the saved preference is different
354 * to the default setting
357 public static boolean getDefault(String property, boolean def)
359 String string = getProperty(property);
362 def = Boolean.valueOf(string).booleanValue();
369 * These methods are used when checking if the saved preference is different
370 * to the default setting
372 public static String getDefault(String property, String def)
374 String string = getProperty(property);
384 * Stores property in the file "HOME_DIR/.jalview_properties"
389 * String value of property
391 * @return String value of property
393 public static String setProperty(String key, String obj)
397 FileOutputStream out = new FileOutputStream(propertiesFile);
398 applicationProperties.setProperty(key, obj);
399 applicationProperties.store(out, "---JalviewX Properties File---");
401 } catch (Exception ex)
403 System.out.println("Error setting property: " + key + " " + obj
409 public static void saveProperties()
413 FileOutputStream out = new FileOutputStream(propertiesFile);
414 applicationProperties.store(out, "---JalviewX Properties File---");
416 } catch (Exception ex)
418 System.out.println("Error saving properties: " + ex);
423 * internal vamsas class discovery state
425 private static int vamsasJarsArePresent = -1;
428 * Searches for vamsas client classes on class path.
430 * @return true if vamsas client is present on classpath
432 public static boolean vamsasJarsPresent()
434 if (vamsasJarsArePresent == -1)
438 if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
439 "uk.ac.vamsas.client.VorbaId") != null)
441 jalview.bin.Cache.log
442 .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
443 vamsasJarsArePresent = 1;
444 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
445 lvclient.setLevel(Level.toLevel(Cache.getDefault(
446 "logs.Vamsas.Level", Level.INFO.toString())));
448 lvclient.addAppender(log.getAppender("JalviewLogger"));
449 // Tell the user that debug is enabled
450 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
452 } catch (Exception e)
454 vamsasJarsArePresent = 0;
455 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
458 return (vamsasJarsArePresent > 0);
462 * internal vamsas class discovery state
464 private static int groovyJarsArePresent = -1;
467 * Searches for vamsas client classes on class path.
469 * @return true if vamsas client is present on classpath
471 public static boolean groovyJarsPresent()
473 if (groovyJarsArePresent == -1)
477 if (Cache.class.getClassLoader().loadClass(
478 "groovy.lang.GroovyObject") != null)
480 jalview.bin.Cache.log
481 .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
482 groovyJarsArePresent = 1;
483 Logger lgclient = Logger.getLogger("groovy");
484 lgclient.setLevel(Level.toLevel(Cache.getDefault(
485 "logs.Groovy.Level", Level.INFO.toString())));
487 lgclient.addAppender(log.getAppender("JalviewLogger"));
488 // Tell the user that debug is enabled
489 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
491 } catch (Exception e)
493 groovyJarsArePresent = 0;
494 jalview.bin.Cache.log.debug("Groovy Classes are not present");
497 return (groovyJarsArePresent > 0);
501 * generate Das1Sources from the local das source list
502 * @return Vector of Das1Sources
504 public static Vector getLocalDasSources()
506 Vector localSources = new Vector();
507 String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
510 StringTokenizer st = new StringTokenizer(local, "\t");
511 while (st.hasMoreTokens())
513 String token = st.nextToken();
514 int bar = token.indexOf("|");
515 Das1Source source = new Das1Source();
516 source.setUrl(token.substring(bar + 1));
517 if (source.getUrl().startsWith("sequence:"))
519 source.setUrl(source.getUrl().substring(9));
520 // this source also serves sequences as well as features
521 source.setCapabilities(new String[] { "sequence", "features"});
523 // default is that all user added sources serve features
524 source.setCapabilities(new String[] { "features"});
527 source.setNickname(token.substring(0, bar));
529 localSources.addElement(source);
535 * GA tracker object - null if tracking not enabled.
537 protected static JGoogleAnalyticsTracker tracker=null;
539 * Initialise the google tracker if it is not done already.
541 public static void initGoogleTracker()
545 String vrs="No Version Accessible";
547 //Google analytics tracking code for Library Finder
548 tracker = new JGoogleAnalyticsTracker("Jalview Desktop",
549 (vrs=jalview.bin.Cache.getProperty("VERSION")+"_"+jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")),
551 tracker.trackAsynchronously(new FocusPoint("Application Started."));
552 } catch (RuntimeException e)
555 log.debug("Caught runtime exception in googletracker init:",e);
564 log.warn("Failed to initialise GoogleTracker for Jalview Desktop with version "+vrs,e);
566 log.warn("Failed to initialise GoogleTracker for Jalview Desktop with version "+vrs,e);