2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 jalview.ws.dbsources.das.api.DasSourceRegistryI;
21 import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
23 import java.awt.Color;
25 import java.text.DateFormat;
26 import java.text.SimpleDateFormat;
29 import org.apache.log4j.*;
32 * Stores and retrieves Jalview Application Properties Lists and fields within
33 * list entries are separated by '|' symbols unless otherwise stated (|) clauses
34 * are alternative values for a tag. <br>
36 * Current properties include:
39 * logs.Axis.Level - one of the stringified Levels for log4j controlling the
40 * logging level for axis (used for web services) <br>
42 * <li>logs.Castor.Level - one of the stringified Levels for log4j controlling
43 * the logging level for castor (used for serialization) <br>
45 * <li>logs.Jalview.Level - Cache.log stringified level. <br>
47 * <li>SCREEN_WIDTH</li>
48 * <li>SCREEN_HEIGHT</li>
49 * <li>SCREEN_Y=285</li>
50 * <li>SCREEN_X=371</li>
51 * <li>SHOW_FULLSCREEN boolean</li>
52 * <li>FONT_NAME java font name for alignment text display</li>
53 * <li>FONT_SIZE size of displayed alignment text</li>
54 * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
55 * <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
56 * <li>LAST_DIRECTORY last directory for browsing alignment</li>
57 * <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
58 * <li>SHOW_FULL_ID show id with '/start-end' numbers appended</li>
59 * <li>SHOW_IDENTITY show percentage identity annotation</li>
60 * <li>SHOW_QUALITY show alignment quality annotation</li>
61 * <li>SHOW_ANNOTATIONS show alignment annotation rows</li>
62 * <li>SHOW_CONSERVATION show alignment conservation annotation</li>
63 * <li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed
65 * <li>DEFAULT_COLOUR default colour scheme to apply for a new alignment</li>
66 * <li>DEFAULT_FILE_FORMAT file format used to save</li>
67 * <li>STARTUP_FILE file loaded on startup (may be a fully qualified url)</li>
68 * <li>SHOW_STARTUP_FILE flag to control loading of startup file</li>
69 * <li>VERSION the version of the jalview build</li>
70 * <li>BUILD_DATE date of this build</li>
71 * <li>LATEST_VERSION the latest jalview version advertised on the
72 * www.jalview.org</li>
73 * <li>PIR_MODELLER boolean indicating if PIR files are written with MODELLER
75 * <li>(FASTA,MSF,PILEUP,CLUSTAL,BLC,PIR,PFAM)_JVSUFFIX boolean for adding jv
77 * <li>RECENT_URL list of recently retrieved URLs</li>
78 * <li>RECENT_FILE list of recently opened files</li>
79 * <li>USE_PROXY flag for whether a http proxy is to be used</li>
80 * <li>PROXY_SERVER the proxy</li>
82 * <li>NOQUESTIONNAIRES true to prevent jalview from checking the questionnaire
84 * <li>QUESTIONNAIRE last questionnaire:responder id string from questionnaire
86 * <li>USAGESTATS (false - user prompted) Enable google analytics tracker for
87 * collecting usage statistics</li>
88 * <li>DAS_LOCAL_SOURCE list of local das sources</li>
89 * <li>SHOW_OVERVIEW boolean for overview window display</li>
90 * <li>ANTI_ALIAS boolean for smooth fonts</li>
91 * <li>RIGHT_ALIGN_IDS boolean</li>
92 * <li>AUTO_CALC_CONSENSUS boolean for automatic recalculation of consensus</li>
93 * <li>PAD_GAPS boolean</li>
94 * <li>ID_ITALICS boolean</li>
95 * <li>SHOW_JV_SUFFIX</li>
96 * <li>WRAP_ALIGNMENT</li>
97 * <li>EPS_RENDERING (Prompt each time|Lineart|Text) default for EPS rendering
99 * <li>SORT_ALIGNMENT (No sort|Id|Pairwise Identity)</li>
100 * <li>SEQUENCE_LINKS list of name|URL pairs for opening a url with
102 * <li>GROUP_LINKS list of name|URL[|<separator>] tuples - see
103 * jalview.utils.GroupURLLink for more info</li>
104 * <li>DAS_REGISTRY_URL the registry to query</li>
105 * <li>DEFAULT_BROWSER for unix</li>
106 * <li>DAS_ACTIVE_SOURCE list of active sources</li>
107 * <li>SHOW_MEMUSAGE boolean show memory usage and warning indicator on desktop
109 * <li>VERSION_CHECK (true) check for the latest release version from
110 * www.jalview.org (or the alias given by the www.jalview.org property)</li>
111 * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence
113 * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence
115 * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved
116 * displayed as '.'</li>
117 * <li>SORT_BY_TREE (false) sort the current alignment view according to the
118 * order of a newly displayed tree</li>
119 * <li>DBFETCH_USEPICR (false) use PICR to recover valid DB references from
120 * sequence ID strings before attempting retrieval from any datasource</li>
121 * <li>SHOW_GROUP_CONSENSUS (false) Show consensus annotation for groups in the
123 * <li>SHOW_GROUP_CONSERVATION (false) Show conservation annotation for groups
124 * in the alignment.</li>
125 * <li>SHOW_CONSENSUS_HISTOGRAM (false) Show consensus annotation row's
127 * <li>SHOW_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
129 * <li>NORMALISE_CONSENSUS_LOGO (false) Show consensus annotation row's sequence
130 * logo normalised to row height rather than histogram height.</li>
131 * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
132 * respond to selections made in other alignments containing the same sequences.
134 * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
135 * warning dialog box is displayed.</li>
136 * <li>ANNOTATIONCOLOUR_MIN (orange) Shade used for minimum value of annotation
137 * when shading by annotation</li>
138 * <li>ANNOTATIONCOLOUR_MAX (red) Shade used for maximum value of annotation
139 * when shading by annotation</li>
140 * <li>www.jalview.org (http://www.jalview.org) a property enabling all HTTP
141 * requests to be redirected to a mirror of http://www.jalview.org</li>
143 * <li>FIGURE_AUTOIDWIDTH (false) Expand the left hand column of an exported
144 * alignment figure to accommodate even the longest sequence ID or annotation
146 * <li>FIGURE_FIXEDIDWIDTH Specifies the width to use for the left-hand column
147 * when exporting an alignment as a figure (setting FIGURE_AUTOIDWIDTH to true
148 * will override this).</li>
152 * Deprecated settings:
155 * <li>DISCOVERY_START - Boolean - controls if discovery services are queried on
156 * startup (JWS1 services only)</li>
157 * <li>DISCOVERY_URLS - comma separated list of Discovery Service endpoints.
158 * (JWS1 services only)</li>
159 * <li>SHOW_JWS1_SERVICES (true) enable or disable the original Jalview 2
160 * services in the desktop GUI</li>
161 * <li>ENABLE_RSBS_EDITOR (false for 2.7 release) enable or disable RSBS editing
162 * panel in web service preferences</li>
166 * @version $Revision$
171 * property giving log4j level for CASTOR loggers
173 public static final String CASTORLOGLEVEL = "logs.Castor.level";
176 * property giving log4j level for AXIS loggers
178 public static final String AXISLOGLEVEL = "logs.Axis.level";
181 * property giving log4j level for Jalview Log
183 public static final String JALVIEWLOGLEVEL = "logs.Jalview.level";
185 public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE";
187 public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL";
189 public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
192 * Initialises the Jalview Application Log
194 public static Logger log;
196 /** Jalview Properties */
197 public static Properties applicationProperties = new Properties();
199 /** Default file is ~/.jalview_properties */
200 static String propertiesFile;
202 private static boolean propsAreReadOnly = false;
204 public static void initLogger()
212 // TODO: redirect stdout and stderr here in order to grab the output of
215 ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
217 ap.setName("JalviewLogger");
218 org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
220 Logger laxis = Logger.getLogger("org.apache.axis");
221 Logger lcastor = Logger.getLogger("org.exolab.castor");
222 jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
224 laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
225 Level.INFO.toString())));
226 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
227 Level.INFO.toString())));
228 lcastor = Logger.getLogger("org.exolab.castor.xml");
229 lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
230 Level.INFO.toString())));
231 // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
232 // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
233 // Level.INFO.toString())));
234 jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
235 "logs.Jalview.level", Level.INFO.toString())));
236 // laxis.addAppender(ap);
237 // lcastor.addAppender(ap);
238 // jalview.bin.Cache.log.addAppender(ap);
239 // Tell the user that debug is enabled
240 jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
241 } catch (Exception ex)
243 System.err.println("Problems initializing the log4j system\n");
244 ex.printStackTrace(System.err);
248 /** Called when Jalview is started */
249 public static void loadProperties(String propsFile)
251 propertiesFile = propsFile;
252 if (propsFile == null)
254 propertiesFile = System.getProperty("user.home") + File.separatorChar
255 + ".jalview_properties";
259 // don't corrupt the file we've been given.
260 propsAreReadOnly = true;
268 fis = new java.net.URL(propertiesFile).openStream();
269 System.out.println("Loading jalview properties from : "
272 .println("Disabling Jalview writing to user's local properties file.");
273 propsAreReadOnly = true;
275 } catch (Exception ex)
281 fis = new FileInputStream(propertiesFile);
283 applicationProperties.load(fis);
284 applicationProperties.remove("LATEST_VERSION");
285 applicationProperties.remove("VERSION");
287 } catch (Exception ex)
289 System.out.println("Error reading properties file: " + ex);
292 if (getDefault("USE_PROXY", false))
294 String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
295 "PROXY_PORT", "8080");
297 System.out.println("Using proxyServer: " + proxyServer
298 + " proxyPort: " + proxyPort);
300 System.setProperty("http.proxyHost", proxyServer);
301 System.setProperty("http.proxyPort", proxyPort);
304 // LOAD THE AUTHORS FROM THE authors.props file
307 String authorDetails = "jar:".concat(Cache.class
308 .getProtectionDomain().getCodeSource().getLocation()
309 .toString().concat("!/authors.props"));
311 java.net.URL localJarFileURL = new java.net.URL(authorDetails);
313 InputStream in = localJarFileURL.openStream();
314 applicationProperties.load(in);
316 } catch (Exception ex)
318 System.out.println("Error reading author details: " + ex);
319 applicationProperties.remove("AUTHORS");
320 applicationProperties.remove("AUTHORFNAMES");
321 applicationProperties.remove("YEAR");
324 // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar
325 // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE
326 // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW
329 String buildDetails = "jar:".concat(Cache.class.getProtectionDomain()
330 .getCodeSource().getLocation().toString()
331 .concat("!/.build_properties"));
333 java.net.URL localJarFileURL = new java.net.URL(buildDetails);
335 InputStream in = localJarFileURL.openStream();
336 applicationProperties.load(in);
338 } catch (Exception ex)
340 System.out.println("Error reading build details: " + ex);
341 applicationProperties.remove("VERSION");
344 String jnlpVersion = System.getProperty("jalview.version");
345 String codeVersion = getProperty("VERSION");
347 if (codeVersion == null)
349 // THIS SHOULD ONLY BE THE CASE WHEN TESTING!!
350 codeVersion = "Test";
351 jnlpVersion = "Test";
354 System.out.println("Jalview Version: " + codeVersion);
356 // jnlpVersion will be null if we're using InstallAnywhere
357 // Dont do this check if running in headless mode
358 if (jnlpVersion == null
359 && getDefault("VERSION_CHECK", true)
360 && (System.getProperty("java.awt.headless") == null || System
361 .getProperty("java.awt.headless").equals("false")))
364 class VersionChecker extends Thread
368 String orgtimeout = System
369 .getProperty("sun.net.client.defaultConnectTimeout");
370 if (orgtimeout == null)
373 System.out.println("# INFO: Setting default net timeout to "
374 + orgtimeout + " seconds.");
376 String jnlpVersion = null;
379 System.setProperty("sun.net.client.defaultConnectTimeout",
381 java.net.URL url = new java.net.URL(Cache.getDefault(
382 "www.jalview.org", "http://www.jalview.org")
383 + "/webstart/jalview.jnlp");
384 BufferedReader in = new BufferedReader(new InputStreamReader(
387 while ((line = in.readLine()) != null)
389 if (line.indexOf("jalview.version") == -1)
394 line = line.substring(line.indexOf("value=") + 7);
395 line = line.substring(0, line.lastIndexOf("\""));
399 } catch (Exception ex)
402 .println("Non-fatal exceptions when checking version at www.jalview.org :");
403 System.out.println(ex);
404 jnlpVersion = getProperty("VERSION");
406 System.setProperty("sun.net.client.defaultConnectTimeout",
409 setProperty("LATEST_VERSION", jnlpVersion);
413 VersionChecker vc = new VersionChecker();
418 if (jnlpVersion != null)
420 setProperty("LATEST_VERSION", jnlpVersion);
424 applicationProperties.remove("LATEST_VERSION");
428 setProperty("VERSION", codeVersion);
430 // LOAD USERDEFINED COLOURS
431 jalview.gui.UserDefinedColours
432 .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
433 jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
438 * Gets Jalview application property of given key. Returns null if key not
444 * @return Property value
446 public static String getProperty(String key)
448 return applicationProperties.getProperty(key);
452 * These methods are used when checking if the saved preference is different
453 * to the default setting
456 public static boolean getDefault(String property, boolean def)
458 String string = getProperty(property);
461 def = Boolean.valueOf(string).booleanValue();
468 * These methods are used when checking if the saved preference is different
469 * to the default setting
471 public static String getDefault(String property, String def)
473 String string = getProperty(property);
483 * Stores property in the file "HOME_DIR/.jalview_properties"
488 * String value of property
490 * @return String value of property
492 public static String setProperty(String key, String obj)
497 applicationProperties.setProperty(key, obj);
498 if (!propsAreReadOnly)
500 FileOutputStream out = new FileOutputStream(propertiesFile);
501 applicationProperties.store(out, "---JalviewX Properties File---");
504 } catch (Exception ex)
506 System.out.println("Error setting property: " + key + " " + obj
513 * remove the specified property from the jalview properties file
517 public static void removeProperty(String string)
519 applicationProperties.remove(string);
524 * save the properties to the jalview properties path
526 public static void saveProperties()
528 if (!propsAreReadOnly)
532 FileOutputStream out = new FileOutputStream(propertiesFile);
533 applicationProperties.store(out, "---JalviewX Properties File---");
535 } catch (Exception ex)
537 System.out.println("Error saving properties: " + ex);
543 * internal vamsas class discovery state
545 private static int vamsasJarsArePresent = -1;
548 * Searches for vamsas client classes on class path.
550 * @return true if vamsas client is present on classpath
552 public static boolean vamsasJarsPresent()
554 if (vamsasJarsArePresent == -1)
558 if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
559 "uk.ac.vamsas.client.VorbaId") != null)
561 jalview.bin.Cache.log
562 .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
563 vamsasJarsArePresent = 1;
564 Logger lvclient = Logger.getLogger("uk.ac.vamsas");
565 lvclient.setLevel(Level.toLevel(Cache.getDefault(
566 "logs.Vamsas.Level", Level.INFO.toString())));
568 lvclient.addAppender(log.getAppender("JalviewLogger"));
569 // Tell the user that debug is enabled
570 lvclient.debug("Jalview Vamsas Client Debugging Output Follows.");
572 } catch (Exception e)
574 vamsasJarsArePresent = 0;
575 jalview.bin.Cache.log.debug("Vamsas Classes are not present");
578 return (vamsasJarsArePresent > 0);
582 * internal vamsas class discovery state
584 private static int groovyJarsArePresent = -1;
587 * Searches for vamsas client classes on class path.
589 * @return true if vamsas client is present on classpath
591 public static boolean groovyJarsPresent()
593 if (groovyJarsArePresent == -1)
597 if (Cache.class.getClassLoader().loadClass(
598 "groovy.lang.GroovyObject") != null)
600 jalview.bin.Cache.log
601 .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
602 groovyJarsArePresent = 1;
603 Logger lgclient = Logger.getLogger("groovy");
604 lgclient.setLevel(Level.toLevel(Cache.getDefault(
605 "logs.Groovy.Level", Level.INFO.toString())));
607 lgclient.addAppender(log.getAppender("JalviewLogger"));
608 // Tell the user that debug is enabled
609 lgclient.debug("Jalview Groovy Client Debugging Output Follows.");
613 groovyJarsArePresent = 0;
614 jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
615 } catch (Exception e)
617 groovyJarsArePresent = 0;
618 jalview.bin.Cache.log.debug("Groovy Classes are not present");
621 return (groovyJarsArePresent > 0);
625 * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not
628 protected static Object tracker = null;
630 protected static Class trackerfocus = null;
632 protected static Class jgoogleanalyticstracker = null;
635 * Initialise the google tracker if it is not done already.
637 public static void initGoogleTracker()
641 if (jgoogleanalyticstracker == null)
643 // try to get the tracker class
646 jgoogleanalyticstracker = Cache.class
649 "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
650 trackerfocus = Cache.class.getClassLoader().loadClass(
651 "com.boxysystems.jgoogleanalytics.FocusPoint");
652 } catch (Exception e)
654 log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
656 jgoogleanalyticstracker = null;
661 // now initialise tracker
662 Exception re = null, ex = null;
664 String vrs = "No Version Accessible";
667 // Google analytics tracking code for Library Finder
668 tracker = jgoogleanalyticstracker.getConstructor(new Class[]
669 { String.class, String.class, String.class }).newInstance(
673 (vrs = jalview.bin.Cache.getProperty("VERSION")
675 + jalview.bin.Cache.getDefault("BUILD_DATE",
676 "unknown")), "UA-9060947-1" });
677 jgoogleanalyticstracker.getMethod("trackAsynchronously",
679 { trackerfocus }).invoke(tracker, new Object[]
680 { trackerfocus.getConstructor(new Class[]
681 { String.class }).newInstance(new Object[]
682 { "Application Started." }) });
683 } catch (RuntimeException e)
686 } catch (Exception e)
693 if (re != null || ex != null || err != null)
698 log.debug("Caught runtime exception in googletracker init:", re);
701 "Failed to initialise GoogleTracker for Jalview Desktop with version "
705 "Whilst initing GoogleTracker for Jalview Desktop version "
713 .println("Debug: Caught runtime exception in googletracker init:"
715 re.printStackTrace();
720 .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
722 ex.printStackTrace();
728 .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
730 err.printStackTrace();
736 log.debug("Successfully initialised tracker.");
742 * get the user's default colour if available
748 public static Color getDefaultColour(String property, Color defcolour)
750 String colprop = getProperty(property);
755 Color col = jalview.schemes.ColourSchemeProperty
756 .getAWTColorFromName(colprop);
761 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
762 } catch (Exception ex)
764 log.warn("Couldn't parse '" + colprop + "' as a colour for "
769 return (col == null) ? defcolour : col;
773 * store a colour as a Jalview user default property
778 public static void setColourProperty(String property, Color colour)
780 setProperty(property, jalview.util.Format.getHexString(colour));
783 public static final DateFormat date_format = SimpleDateFormat
784 .getDateTimeInstance();
787 * store a date in a jalview property
792 public static void setDateProperty(String property, Date time)
794 setProperty(property, date_format.format(time));
798 * read a date stored in a jalview property
801 * @return valid date as stored by setDateProperty, or null
804 public static Date getDateProperty(String property)
806 String val = getProperty(property);
811 return date_format.parse(val);
812 } catch (Exception ex)
814 System.err.println("Invalid or corrupt date in property '"
815 + property + "' : value was '" + val + "'");
822 * get and parse a property as an integer. send any parsing problems to
826 * @return null or Integer
828 public static Integer getIntegerProperty(String property)
830 String val = getProperty(property);
831 if (val != null && (val = val.trim()).length() > 0)
835 return Integer.valueOf(val);
836 } catch (NumberFormatException x)
838 System.err.println("Invalid integer in property '" + property
839 + "' (value was '" + val + "')");
845 private static DasSourceRegistryI sourceRegistry = null;
850 * @return instance of the das source registry
852 public static DasSourceRegistryI getDasSourceRegistry()
854 if (sourceRegistry == null)
856 sourceRegistry = new DasSourceRegistry();
858 return sourceRegistry;