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/>.
20 import java.awt.Color;
24 import org.apache.log4j.*;
25 import org.biojava.dasobert.dasregistry.Das1Source;
28 * Stores and retrieves Jalview Application Properties Lists and fields within
29 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
30 * are alternative values for a tag. <br>
32 * Current properties include:
35 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
36 * logging level for axis (used for web services) <br>
38 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
39 * the logging level for castor (used for serialization) <br>
41 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
43 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
45 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.</li>
46 * <li>SCREEN_WIDTH</li>
47 * <li>SCREEN_HEIGHT</li>
48 * <li>SCREEN_Y=285</li>
49 * <li>SCREEN_X=371</li>
50 * <li>SHOW_FULLSCREEN boolean</li>
51 * <li>FONT_NAME java font name for alignment text display</li>
52 * <li>FONT_SIZE size of displayed alignment text</li>
53 * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
54 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
55 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
56 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
57 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
58 * <li>SHOW_IDENTITY show percentage identity annotation</li>
59 * <li>SHOW_QUALITY show alignment quality annotation</li>
60 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
61 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
62 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
64 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
65 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
66 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
67 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
68 * <li>VERSION the version of the jalview build</li>
69 * <li>BUILD_DATE date of this build</li>
70 * <li>LATEST_VERSION the latest jalview version advertised on the
71 * www.jalview.org</li>
72 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
74 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
76 * <li>RECENT_URL list of recently retrieved URLs</li>
77 * <li>RECENT_FILE list of recently opened files</li>
78 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
79 * <li>PROXY_SERVER the proxy</li>
81 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
83 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
85 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
86 * collecting usage statistics</li>
87 * <li>DAS_LOCAL_SOURCE list of local das sources</li>
88 * <li>SHOW_OVERVIEW boolean for overview window display</li>
89 * <li>ANTI_ALIAS boolean for smooth fonts</li>
90 * <li>RIGHT_ALIGN_IDS boolean</li>
91 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
92 * <li>PAD_GAPS boolean</li>
93 * <li>ID_ITALICS boolean</li>
94 * <li>SHOW_JV_SUFFIX</li>
95 * <li>WRAP_ALIGNMENT</li>
96 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
98 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
99 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
101 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
102 * jalview.utils.GroupURLLink for more info</li>
103 * <li>DAS_REGISTRY_URL the registry to query</li>
104 * <li>DEFAULT_BROWSER for unix</li>
105 * <li>DAS_ACTIVE_SOURCE list of active sources</li>
106 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
108 * <li>VERSION_CHECK (true) check for the latest release version from
109 * www.jalview.org</li>
110 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
112 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
114 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
115 * displayed as '.'</li>
116 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
117 * order of a newly displayed tree</li>
118 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
119 * sequence ID strings before attempting retrieval from any datasource</li>
120 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
122 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
123 * in the alignment.</li>
124 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
126 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
128 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
129 * respond to selections made in other alignments containing the same sequences.
131 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
132 * warning dialog box is displayed.</li>
133 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation when shading by annotation</li>
134 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation when shading by annotation</li>
143 * @version $Revision$
148 * property giving log4j level for CASTOR loggers
150 public static final String CASTORLOGLEVEL = "logs.Castor.level";
153 * property giving log4j level for AXIS loggers
155 public static final String AXISLOGLEVEL = "logs.Axis.level";
158 * property giving log4j level for Jalview Log
160 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
162 public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
164 public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
166 public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
169 * Initialises the Jalview Application Log
171 public static Logger log;
173 /** Jalview Properties */
174 public static Properties applicationProperties = new Properties();
176 /** Default file is ~/.jalview_properties */
177 static String propertiesFile;
179 private static boolean propsAreReadOnly=false;
181 public static void initLogger()
189 // TODO: redirect stdout and stderr here in order to grab the output of
192 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
194 ap.setName("JalviewLogger");
195 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
197 Logger laxis = Logger.getLogger("org.apache.axis");
198 Logger lcastor = Logger.getLogger("org.exolab.castor");
199 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
201 laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
202 Level.INFO.toString())));
203 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
204 Level.INFO.toString())));
205 lcastor = Logger.getLogger("org.exolab.castor.xml");
206 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
207 Level.INFO.toString())));
208 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
209 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
210 // Level.INFO.toString())));
211 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
212 "logs.Jalview.level", Level.INFO.toString())));
213 // laxis.addAppender(ap);
214 // lcastor.addAppender(ap);
215 // jalview.bin.Cache.log.addAppender(ap);
216 // Tell the user that debug is enabled
217 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
218 } catch (Exception ex)
220 System.err.println("Problems initializing the log4j system\n");
221 ex.printStackTrace(System.err);
225 /** Called when Jalview is started */
226 public static void loadProperties(String propsFile)
228 propertiesFile = propsFile;
229 if (propsFile == null)
231 propertiesFile = System.getProperty("user.home") + File.separatorChar
232 + ".jalview_properties";
234 // don't corrupt the file we've been given.
235 propsAreReadOnly = true;
243 fis = new java.net.URL(propertiesFile).openStream();
244 System.out.println("Loading jalview properties from : "
247 .println("Disabling Jalview writing to user's local properties file.");
248 propsAreReadOnly = true;
250 } catch (Exception ex)
256 fis = new FileInputStream(propertiesFile);
258 applicationProperties.load(fis);
259 applicationProperties.remove("LATEST_VERSION");
260 applicationProperties.remove("VERSION");
262 } catch (Exception ex)
264 System.out.println("Error reading properties file: " + ex);
267 if (getDefault("USE_PROXY", false))
269 System.out.println("Using proxyServer: "
270 + getDefault("PROXY_SERVER", null) + " proxyPort: "
271 + getDefault("PROXY_PORT", null));
272 System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null));
273 System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null));
276 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
277 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
278 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
281 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
282 .getCodeSource().getLocation().toString()
283 .concat("!/.build_properties"));
285 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
287 InputStream in = localJarFileURL.openStream();
288 applicationProperties.load(in);
290 } catch (Exception ex)
292 System.out.println("Error reading build details: " + ex);
293 applicationProperties.remove("VERSION");
296 String jnlpVersion = System.getProperty("jalview.version");
297 String codeVersion = getProperty("VERSION");
299 if (codeVersion == null)
301 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
302 codeVersion = "Test";
303 jnlpVersion = "Test";
306 System.out.println("Jalview Version: " + codeVersion);
308 // jnlpVersion will be null if we're using InstallAnywhere
309 // Dont do this check if running in headless mode
310 if (jnlpVersion == null
311 && getDefault("VERSION_CHECK", true)
312 && (System.getProperty("java.awt.headless") == null || System
313 .getProperty("java.awt.headless").equals("false")))
316 class VersionChecker extends Thread
320 String orgtimeout = System
321 .getProperty("sun.net.client.defaultConnectTimeout");
322 if (orgtimeout == null)
325 System.out.println("# INFO: Setting default net timeout to "
326 + orgtimeout + " seconds.");
328 String jnlpVersion = null;
331 System.setProperty("sun.net.client.defaultConnectTimeout",
333 java.net.URL url = new java.net.URL(
334 "http://www.jalview.org/webstart/jalview.jnlp");
335 BufferedReader in = new BufferedReader(new InputStreamReader(
338 while ((line = in.readLine()) != null)
340 if (line.indexOf("jalview.version") == -1)
345 line = line.substring(line.indexOf("value=") + 7);
346 line = line.substring(0, line.lastIndexOf("\""));
350 } catch (Exception ex)
353 .println("Non-fatal exceptions when checking version at www.jalview.org :");
354 System.out.println(ex);
355 jnlpVersion = getProperty("VERSION");
357 System.setProperty("sun.net.client.defaultConnectTimeout",
360 setProperty("LATEST_VERSION", jnlpVersion);
364 VersionChecker vc = new VersionChecker();
369 if (jnlpVersion != null)
371 setProperty("LATEST_VERSION", jnlpVersion);
375 applicationProperties.remove("LATEST_VERSION");
379 setProperty("VERSION", codeVersion);
381 // LOAD USERDEFINED COLOURS
382 jalview.gui.UserDefinedColours
383 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
384 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
389 * Gets Jalview application property of given key. Returns null if key not
395 * @return Property value
397 public static String getProperty(String key)
399 return applicationProperties.getProperty(key);
403 * These methods are used when checking if the saved preference is different
404 * to the default setting
407 public static boolean getDefault(String property, boolean def)
409 String string = getProperty(property);
412 def = Boolean.valueOf(string).booleanValue();
419 * These methods are used when checking if the saved preference is different
420 * to the default setting
422 public static String getDefault(String property, String def)
424 String string = getProperty(property);
434 * Stores property in the file "HOME_DIR/.jalview_properties"
439 * String value of property
441 * @return String value of property
443 public static String setProperty(String key, String obj)
448 applicationProperties.setProperty(key, obj);
449 if (!propsAreReadOnly)
451 FileOutputStream out = new FileOutputStream(propertiesFile);
452 applicationProperties.store(out, "---JalviewX Properties File---");
455 } catch (Exception ex)
457 System.out.println("Error setting property: " + key + " " + obj
464 * remove the specified property from the jalview properties file
468 public static void removeProperty(String string)
470 applicationProperties.remove(string);
475 * save the properties to the jalview properties path
477 public static void saveProperties()
479 if (!propsAreReadOnly)
483 FileOutputStream out = new FileOutputStream(propertiesFile);
484 applicationProperties.store(out, "---JalviewX Properties File---");
486 } catch (Exception ex)
488 System.out.println("Error saving properties: " + ex);
494 * internal vamsas class discovery state
496 private static int vamsasJarsArePresent = -1;
499 * Searches for vamsas client classes on class path.
501 * @return true if vamsas client is present on classpath
503 public static boolean vamsasJarsPresent()
505 if (vamsasJarsArePresent == -1)
509 if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
510 "uk.ac.vamsas.client.VorbaId") != null)
512 jalview.bin.Cache.log
513 .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
514 vamsasJarsArePresent = 1;
515 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
516 lvclient.setLevel(Level.toLevel(Cache.getDefault(
517 "logs.Vamsas.Level", Level.INFO.toString())));
519 lvclient.addAppender(log.getAppender("JalviewLogger"));
520 // Tell the user that debug is enabled
521 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
523 } catch (Exception e)
525 vamsasJarsArePresent = 0;
526 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
529 return (vamsasJarsArePresent > 0);
533 * internal vamsas class discovery state
535 private static int groovyJarsArePresent = -1;
538 * Searches for vamsas client classes on class path.
540 * @return true if vamsas client is present on classpath
542 public static boolean groovyJarsPresent()
544 if (groovyJarsArePresent == -1)
548 if (Cache.class.getClassLoader().loadClass(
549 "groovy.lang.GroovyObject") != null)
551 jalview.bin.Cache.log
552 .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
553 groovyJarsArePresent = 1;
554 Logger lgclient = Logger.getLogger("groovy");
555 lgclient.setLevel(Level.toLevel(Cache.getDefault(
556 "logs.Groovy.Level", Level.INFO.toString())));
558 lgclient.addAppender(log.getAppender("JalviewLogger"));
559 // Tell the user that debug is enabled
560 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
564 groovyJarsArePresent = 0;
565 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
566 } catch (Exception e)
568 groovyJarsArePresent = 0;
569 jalview.bin.Cache.log.debug("Groovy Classes are not present");
572 return (groovyJarsArePresent > 0);
576 * generate Das1Sources from the local das source list
578 * @return Vector of Das1Sources
580 public static Vector getLocalDasSources()
582 Vector localSources = new Vector();
583 String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
586 StringTokenizer st = new StringTokenizer(local, "\t");
587 while (st.hasMoreTokens())
589 String token = st.nextToken();
590 int bar = token.indexOf("|");
591 Das1Source source = new Das1Source();
592 source.setUrl(token.substring(bar + 1));
593 if (source.getUrl().startsWith("sequence:"))
595 source.setUrl(source.getUrl().substring(9));
596 // this source also serves sequences as well as features
597 source.setCapabilities(new String[]
598 { "sequence", "features" });
602 // default is that all user added sources serve features
603 source.setCapabilities(new String[]
607 source.setNickname(token.substring(0, bar));
609 localSources.addElement(source);
616 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
619 protected static Object tracker = null;
621 protected static Class trackerfocus = null;
623 protected static Class jgoogleanalyticstracker = null;
626 * Initialise the google tracker if it is not done already.
628 public static void initGoogleTracker()
632 if (jgoogleanalyticstracker == null)
634 // try to get the tracker class
637 jgoogleanalyticstracker = Cache.class
640 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
641 trackerfocus = Cache.class.getClassLoader().loadClass(
642 "com.boxysystems.jgoogleanalytics.FocusPoint");
643 } catch (Exception e)
645 log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
647 jgoogleanalyticstracker = null;
652 // now initialise tracker
653 Exception re = null, ex = null;
655 String vrs = "No Version Accessible";
658 // Google analytics tracking code for Library Finder
659 tracker = jgoogleanalyticstracker.getConstructor(new Class[]
660 { String.class, String.class, String.class }).newInstance(
664 (vrs = jalview.bin.Cache.getProperty("VERSION")
666 + jalview.bin.Cache.getDefault("BUILD_DATE",
667 "unknown")), "UA-9060947-1" });
668 jgoogleanalyticstracker.getMethod("trackAsynchronously",
670 { trackerfocus }).invoke(tracker, new Object[]
671 { trackerfocus.getConstructor(new Class[]
672 { String.class }).newInstance(new Object[]
673 { "Application Started." }) });
674 } catch (RuntimeException e)
677 } catch (Exception e)
684 if (re != null || ex != null || err != null)
689 log.debug("Caught runtime exception in googletracker init:", re);
692 "Failed to initialise GoogleTracker for Jalview Desktop with version "
696 "Whilst initing GoogleTracker for Jalview Desktop version "
704 .println("Debug: Caught runtime exception in googletracker init:"
706 re.printStackTrace();
711 .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
713 ex.printStackTrace();
719 .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
721 err.printStackTrace();
727 log.debug("Successfully initialised tracker.");
733 * get the user's default colour if available
738 public static Color getDefaultColour(String property, Color defcolour)
740 String colprop = getProperty(property);
744 Color col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName(colprop);
748 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
749 } catch (Exception ex)
751 log.warn("Couldn't parse '"+colprop+"' as a colour for "+property);
755 return (col==null) ? defcolour: col;