X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=63a34123e553add043d5cde5d2553befa4e48b55;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=1b5ba56e70a5ce72899e98fd195b731dc04d4dc6;hpb=a91379944accf50c8dc0082c61e399dffbd7287a;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 1b5ba56..63a3412 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,329 +1,825 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.bin; +import java.awt.Color; import java.io.*; - +import java.text.DateFormat; +import java.text.SimpleDateFormat; import java.util.*; -import org.apache.log4j.Logger; -import org.apache.log4j.SimpleLayout; -import org.apache.log4j.Level; -import org.apache.log4j.ConsoleAppender; - +import org.apache.log4j.*; +import org.biojava.dasobert.dasregistry.Das1Source; /** - * Stores and retrieves Jalview Application Properties - *

Current properties include: - *
logs.Axis.Level - one of the stringified Levels for log4j controlling the logging level for axis (used for web services) - *
logs.Castor.Level - one of the stringified Levels for log4j controlling the logging level for castor (used for serialization) - *
logs.Jalview.Level - Cache.log stringified level. - *
DISCOVERY_START - Boolean - controls if discovery services are queried on startup - *
DISCOVERY_URLS - comma separated list of Discovery Service endpoints. - *
SCREEN_WIDTH,SCREEN_HEIGHT,SCREEN_Y=285,SCREEN_X=371,SHOW_FULLSCREEN - * FONT_NAME,FONT_SIZE,FONT_STYLE,GAP_SYMBOL,LAST_DIRECTORY,USER_DEFINED_COLOUR - * SHOW_FULL_ID,SHOW_IDENTITY,SHOW_QUALITY,SHOW_ANNOTATIONS,SHOW_CONSERVATION, - * DEFAULT_COLOUR,DEFAULT_FILE_FORMAT,STARTUP_FILE,SHOW_STARTUP_FILE - + * Stores and retrieves Jalview Application Properties Lists and fields within + * list entries are separated by '|' symbols unless otherwise stated (|) clauses + * are alternative values for a tag.
+ *
+ * Current properties include: + * + * Deprecated settings: + * * @author $author$ * @version $Revision$ */ public class Cache { /** - * Initialises the Apache Axis logger + * property giving log4j level for CASTOR loggers + */ + public static final String CASTORLOGLEVEL = "logs.Castor.level"; + + /** + * property giving log4j level for AXIS loggers + */ + public static final String AXISLOGLEVEL = "logs.Axis.level"; + + /** + * property giving log4j level for Jalview Log + */ + public static final String JALVIEWLOGLEVEL = "logs.Jalview.level"; + + public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE"; + + public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL"; + + public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE"; + + /** + * Initialises the Jalview Application Log */ public static Logger log; - /** Jalview Properties */ - public static Properties applicationProperties = new Properties(); + /** Jalview Properties */ + public static Properties applicationProperties = new Properties(); + + /** Default file is ~/.jalview_properties */ + static String propertiesFile; + + private static boolean propsAreReadOnly=false; + + public static void initLogger() + { + if (log != null) + { + return; + } + try + { + // TODO: redirect stdout and stderr here in order to grab the output of + // the log + + ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(), + "System.err"); + ap.setName("JalviewLogger"); + org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for + // log output + Logger laxis = Logger.getLogger("org.apache.axis"); + Logger lcastor = Logger.getLogger("org.exolab.castor"); + jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview"); + + laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level", + Level.INFO.toString()))); + lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", + Level.INFO.toString()))); + lcastor = Logger.getLogger("org.exolab.castor.xml"); + lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", + Level.INFO.toString()))); + // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller"); + // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", + // Level.INFO.toString()))); + jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault( + "logs.Jalview.level", Level.INFO.toString()))); + // laxis.addAppender(ap); + // lcastor.addAppender(ap); + // jalview.bin.Cache.log.addAppender(ap); + // Tell the user that debug is enabled + jalview.bin.Cache.log.debug("Jalview Debugging Output Follows."); + } catch (Exception ex) + { + System.err.println("Problems initializing the log4j system\n"); + ex.printStackTrace(System.err); + } + } - /** Default file is ~/.jalview_properties */ - static String propertiesFile; + /** Called when Jalview is started */ + public static void loadProperties(String propsFile) + { + propertiesFile = propsFile; + if (propsFile == null) + { + propertiesFile = System.getProperty("user.home") + File.separatorChar + + ".jalview_properties"; + } else { + // don't corrupt the file we've been given. + propsAreReadOnly = true; + } - public static void initLogger() + try { + InputStream fis; try { - Logger laxis = Logger.getLogger("org.apache.axis"); - Logger lcastor = Logger.getLogger("org.exolab.castor"); - jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview"); - - laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level", - Level.INFO.toString()))); - lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", - Level.INFO.toString()))); - jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault( - "logs.Jalview.level", - Level.INFO.toString()))); - ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(), - "System.err"); - ap.setName("JalviewLogger"); - - laxis.addAppender(ap); - lcastor.addAppender(ap); - jalview.bin.Cache.log.addAppender(ap); - // Tell the user that debug is enabled - jalview.bin.Cache.log.debug("Jalview Debugging Output Follows."); + fis = new java.net.URL(propertiesFile).openStream(); + System.out.println("Loading jalview properties from : " + + propertiesFile); + System.out + .println("Disabling Jalview writing to user's local properties file."); + propsAreReadOnly = true; + + } catch (Exception ex) + { + fis = null; } - catch (Exception ex) + if (fis == null) { - System.err.println("Problems initializing the log4j system\n"); + fis = new FileInputStream(propertiesFile); } + applicationProperties.load(fis); + applicationProperties.remove("LATEST_VERSION"); + applicationProperties.remove("VERSION"); + fis.close(); + } catch (Exception ex) + { + System.out.println("Error reading properties file: " + ex); } + if (getDefault("USE_PROXY", false)) + { + System.out.println("Using proxyServer: " + + getDefault("PROXY_SERVER", null) + " proxyPort: " + + getDefault("PROXY_PORT", null)); + System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null)); + System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null)); + } - /** Called when Jalview is started */ - public static void loadProperties(String propsFile) + // LOAD THE AUTHORS FROM THE authors.props file + try { - propertiesFile = propsFile; - if (propsFile == null) - { - propertiesFile = System.getProperty("user.home") + "/.jalview_properties"; - } + String authorDetails = "jar:".concat(Cache.class.getProtectionDomain() + .getCodeSource().getLocation().toString() + .concat("!/authors.props")); - try - { - FileInputStream fis = new FileInputStream(propertiesFile); - applicationProperties.load(fis); - applicationProperties.remove("LATEST_VERSION"); - applicationProperties.remove("VERSION"); - fis.close(); - } - catch (Exception ex) - { - System.out.println("Error reading properties file: "+ex); - } + java.net.URL localJarFileURL = new java.net.URL(authorDetails); - if(getDefault("USE_PROXY", false)) - { - System.out.println("Using proxyServer: "+getDefault("PROXY_SERVER", null)+ - " proxyPort: "+getDefault("PROXY_PORT", null)); - System.setProperty("http.proxyHost", getDefault("PROXY_SERVER", null)); - System.setProperty("http.proxyPort", getDefault("PROXY_PORT", null)); - } + InputStream in = localJarFileURL.openStream(); + applicationProperties.load(in); + in.close(); + } catch (Exception ex) + { + System.out.println("Error reading author details: " + ex); + applicationProperties.remove("AUTHORS"); + applicationProperties.remove("AUTHORFNAMES"); + applicationProperties.remove("YEAR"); + } - // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar - // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE - // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW - try - { - String buildDetails = "jar:" - .concat( - Cache.class.getProtectionDomain().getCodeSource().getLocation().toString() - .concat("!/.build_properties") - ); - - java.net.URL localJarFileURL = new java.net.URL(buildDetails); - - InputStream in = localJarFileURL.openStream(); - applicationProperties.load(in); - in.close(); - } - catch (Exception ex) - { - System.out.println("Error reading build details: "+ex); - applicationProperties.remove("VERSION"); - } + // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar + // MUST FOLLOW READING OF LOCAL PROPERTIES FILE AS THE + // VERSION MAY HAVE CHANGED SINCE LAST USING JALVIEW + try + { + String buildDetails = "jar:".concat(Cache.class.getProtectionDomain() + .getCodeSource().getLocation().toString() + .concat("!/.build_properties")); - String jnlpVersion = System.getProperty("jalview.version"); - String codeVersion = getProperty("VERSION"); + java.net.URL localJarFileURL = new java.net.URL(buildDetails); + InputStream in = localJarFileURL.openStream(); + applicationProperties.load(in); + in.close(); + } catch (Exception ex) + { + System.out.println("Error reading build details: " + ex); + applicationProperties.remove("VERSION"); + } - if(codeVersion==null) - { - // THIS SHOULD ONLY BE THE CASE WHEN TESTING!! - codeVersion = "Test"; - jnlpVersion = "Test"; - } + String jnlpVersion = System.getProperty("jalview.version"); + String codeVersion = getProperty("VERSION"); + if (codeVersion == null) + { + // THIS SHOULD ONLY BE THE CASE WHEN TESTING!! + codeVersion = "Test"; + jnlpVersion = "Test"; + } - System.out.println("Jalview Version: "+codeVersion); + System.out.println("Jalview Version: " + codeVersion); + // jnlpVersion will be null if we're using InstallAnywhere + // Dont do this check if running in headless mode + if (jnlpVersion == null + && getDefault("VERSION_CHECK", true) + && (System.getProperty("java.awt.headless") == null || System + .getProperty("java.awt.headless").equals("false"))) + { - // jnlpVersion will be null if we're using InstallAnywhere - // Dont do this check if running in headless mode - if(jnlpVersion==null && ( - System.getProperty("java.awt.headless")==null - || System.getProperty("java.awt.headless").equals("false"))) + class VersionChecker extends Thread + { + public void run() { - - class VersionChecker - extends Thread + String orgtimeout = System + .getProperty("sun.net.client.defaultConnectTimeout"); + if (orgtimeout == null) + { + orgtimeout = "30"; + System.out.println("# INFO: Setting default net timeout to " + + orgtimeout + " seconds."); + } + String jnlpVersion = null; + try { - public void run() + System.setProperty("sun.net.client.defaultConnectTimeout", + "5000"); + java.net.URL url = new java.net.URL( + Cache.getDefault("www.jalview.org", "http://www.jalview.org")+"/webstart/jalview.jnlp"); + BufferedReader in = new BufferedReader(new InputStreamReader( + url.openStream())); + String line = null; + while ((line = in.readLine()) != null) { - String jnlpVersion = null; - try - { - java.net.URL url = new java.net.URL( - "http://www.jalview.org/webstart/jalview.jnlp"); - BufferedReader in = new BufferedReader(new InputStreamReader(url. - openStream())); - String line = null; - while ( (line = in.readLine()) != null) - { - if (line.indexOf("jalview.version") == -1) - continue; - - line = line.substring(line.indexOf("value=") + 7); - line = line.substring(0, line.lastIndexOf("\"")); - jnlpVersion = line; - break; - } - } - catch (Exception ex) + if (line.indexOf("jalview.version") == -1) { - System.out.println(ex); - jnlpVersion = getProperty("VERSION"); + continue; } - setProperty("LATEST_VERSION", jnlpVersion); + line = line.substring(line.indexOf("value=") + 7); + line = line.substring(0, line.lastIndexOf("\"")); + jnlpVersion = line; + break; } + } catch (Exception ex) + { + System.out + .println("Non-fatal exceptions when checking version at www.jalview.org :"); + System.out.println(ex); + jnlpVersion = getProperty("VERSION"); } + System.setProperty("sun.net.client.defaultConnectTimeout", + orgtimeout); - VersionChecker vc = new VersionChecker(); - vc.start(); - } - else - { - if(jnlpVersion!=null) - setProperty("LATEST_VERSION", jnlpVersion); - else - applicationProperties.remove("LATEST_VERSION"); + setProperty("LATEST_VERSION", jnlpVersion); } + } - setProperty("VERSION", codeVersion); - - //LOAD USERDEFINED COLOURS - jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS")); - jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false); + VersionChecker vc = new VersionChecker(); + vc.start(); } + else + { + if (jnlpVersion != null) + { + setProperty("LATEST_VERSION", jnlpVersion); + } + else + { + applicationProperties.remove("LATEST_VERSION"); + } + } + + setProperty("VERSION", codeVersion); + + // LOAD USERDEFINED COLOURS + jalview.gui.UserDefinedColours + .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS")); + jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", + false); + } + + /** + * Gets Jalview application property of given key. Returns null if key not + * found + * + * @param key + * Name of property + * + * @return Property value + */ + public static String getProperty(String key) + { + return applicationProperties.getProperty(key); + } + /** + * These methods are used when checking if the saved preference is different + * to the default setting + */ + + public static boolean getDefault(String property, boolean def) + { + String string = getProperty(property); + if (string != null) + { + def = Boolean.valueOf(string).booleanValue(); + } + return def; + } - /** - * Gets Jalview application property of given key. Returns null - * if key not found - * - * @param key Name of property - * - * @return Property value - */ - public static String getProperty(String key) + /** + * These methods are used when checking if the saved preference is different + * to the default setting + */ + public static String getDefault(String property, String def) + { + String string = getProperty(property); + if (string != null) { - return applicationProperties.getProperty(key); + return string; } + return def; + } - /** These methods are used when checking if the saved preference - * is different to the default setting - */ + /** + * Stores property in the file "HOME_DIR/.jalview_properties" + * + * @param key + * Name of object + * @param obj + * String value of property + * + * @return String value of property + */ + public static String setProperty(String key, String obj) + { - public static boolean getDefault(String property, boolean def) + try { - String string = getProperty(property); - if (string != null) + applicationProperties.setProperty(key, obj); + if (!propsAreReadOnly) { - def = Boolean.valueOf(string).booleanValue(); + FileOutputStream out = new FileOutputStream(propertiesFile); + applicationProperties.store(out, "---JalviewX Properties File---"); + out.close(); } - - return def; + } catch (Exception ex) + { + System.out.println("Error setting property: " + key + " " + obj + + "\n" + ex); } + return obj; + } - /** These methods are used when checking if the saved preference - * is different to the default setting - */ - public static String getDefault(String property, String def) + /** + * remove the specified property from the jalview properties file + * + * @param string + */ + public static void removeProperty(String string) + { + applicationProperties.remove(string); + saveProperties(); + } + + /** + * save the properties to the jalview properties path + */ + public static void saveProperties() + { + if (!propsAreReadOnly) { - String string = getProperty(property); - if (string != null) + try + { + FileOutputStream out = new FileOutputStream(propertiesFile); + applicationProperties.store(out, "---JalviewX Properties File---"); + out.close(); + } catch (Exception ex) { - return string; + System.out.println("Error saving properties: " + ex); } + } + } + + /** + * internal vamsas class discovery state + */ + private static int vamsasJarsArePresent = -1; - return def; + /** + * Searches for vamsas client classes on class path. + * + * @return true if vamsas client is present on classpath + */ + public static boolean vamsasJarsPresent() + { + if (vamsasJarsArePresent == -1) + { + try + { + if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass( + "uk.ac.vamsas.client.VorbaId") != null) + { + jalview.bin.Cache.log + .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)"); + vamsasJarsArePresent = 1; + Logger lvclient = Logger.getLogger("uk.ac.vamsas"); + lvclient.setLevel(Level.toLevel(Cache.getDefault( + "logs.Vamsas.Level", Level.INFO.toString()))); + + lvclient.addAppender(log.getAppender("JalviewLogger")); + // Tell the user that debug is enabled + lvclient.debug("Jalview Vamsas Client Debugging Output Follows."); + } + } catch (Exception e) + { + vamsasJarsArePresent = 0; + jalview.bin.Cache.log.debug("Vamsas Classes are not present"); + } } + return (vamsasJarsArePresent > 0); + } + /** + * internal vamsas class discovery state + */ + private static int groovyJarsArePresent = -1; - /** - * Stores property in the file "HOME_DIR/.jalview_properties" - * - * @param key Name of object - * @param obj String value of property - * - * @return String value of property - */ - public static String setProperty(String key, String obj) + /** + * Searches for vamsas client classes on class path. + * + * @return true if vamsas client is present on classpath + */ + public static boolean groovyJarsPresent() + { + if (groovyJarsArePresent == -1) { - try + try + { + if (Cache.class.getClassLoader().loadClass( + "groovy.lang.GroovyObject") != null) { - FileOutputStream out = new FileOutputStream(propertiesFile); - applicationProperties.setProperty(key, obj); - applicationProperties.store(out, "---JalviewX Properties File---"); - out.close(); + jalview.bin.Cache.log + .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)"); + groovyJarsArePresent = 1; + Logger lgclient = Logger.getLogger("groovy"); + lgclient.setLevel(Level.toLevel(Cache.getDefault( + "logs.Groovy.Level", Level.INFO.toString()))); + + lgclient.addAppender(log.getAppender("JalviewLogger")); + // Tell the user that debug is enabled + lgclient.debug("Jalview Groovy Client Debugging Output Follows."); } - catch (Exception ex) - { System.out.println("Error setting property: "+key+" "+obj+"\n"+ex); } - return obj; + } catch (Error e) + { + groovyJarsArePresent = 0; + jalview.bin.Cache.log.debug("Groovy Classes are not present", e); + } catch (Exception e) + { + groovyJarsArePresent = 0; + jalview.bin.Cache.log.debug("Groovy Classes are not present"); + } } + return (groovyJarsArePresent > 0); + } - public static void saveProperties() + /** + * generate Das1Sources from the local das source list + * + * @return Vector of Das1Sources + */ + public static Vector getLocalDasSources() + { + Vector localSources = new Vector(); + String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE"); + if (local != null) { - try + StringTokenizer st = new StringTokenizer(local, "\t"); + while (st.hasMoreTokens()) + { + String token = st.nextToken(); + int bar = token.indexOf("|"); + Das1Source source = new Das1Source(); + source.setUrl(token.substring(bar + 1)); + if (source.getUrl().startsWith("sequence:")) { - FileOutputStream out = new FileOutputStream(propertiesFile); - applicationProperties.store(out, "---JalviewX Properties File---"); - out.close(); + source.setUrl(source.getUrl().substring(9)); + // this source also serves sequences as well as features + source.setCapabilities(new String[] + { "sequence", "features" }); } - catch (Exception ex) - { System.out.println("Error saving properties: "+ex); } + else + { + // default is that all user added sources serve features + source.setCapabilities(new String[] + { "features" }); + } + + source.setNickname(token.substring(0, bar)); + + localSources.addElement(source); + } } - /** - * internal vamsas class discovery state - */ - private static int vamsasJarsArePresent=-1; - /** - * Searches for vamsas client classes on class path. - * @return true if vamsas client is present on classpath - */ - public static boolean vamsasJarsPresent() { - if (vamsasJarsArePresent==-1) { - try { - if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass("org.vamsas.client.VorbaId")!=null) { - jalview.bin.Cache.log.debug("Found Vamsas Classes (org.vamsas.client.VorbaId can be loaded)"); - vamsasJarsArePresent=1; - Logger lvclient = Logger.getLogger("org.vamsas.client"); - lvclient.setLevel(Level.toLevel(Cache.getDefault("logs.Vamsas.Level", - Level.INFO.toString()))); - ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(), - "System.err"); - lvclient.addAppender(log.getAppender("JalviewLogger")); - // Tell the user that debug is enabled - lvclient.debug("Jalview Vamsas Client Debugging Output Follows."); + return localSources; + } + + /** + * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not + * enabled. + */ + protected static Object tracker = null; + + protected static Class trackerfocus = null; + + protected static Class jgoogleanalyticstracker = null; + + /** + * Initialise the google tracker if it is not done already. + */ + public static void initGoogleTracker() + { + if (tracker == null) + { + if (jgoogleanalyticstracker == null) + { + // try to get the tracker class + try + { + jgoogleanalyticstracker = Cache.class + .getClassLoader() + .loadClass( + "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker"); + trackerfocus = Cache.class.getClassLoader().loadClass( + "com.boxysystems.jgoogleanalytics.FocusPoint"); + } catch (Exception e) + { + log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled."); + tracker = null; + jgoogleanalyticstracker = null; + trackerfocus = null; + return; + } + } + // now initialise tracker + Exception re = null, ex = null; + Error err = null; + String vrs = "No Version Accessible"; + try + { + // Google analytics tracking code for Library Finder + tracker = jgoogleanalyticstracker.getConstructor(new Class[] + { String.class, String.class, String.class }).newInstance( + new Object[] + { + "Jalview Desktop", + (vrs = jalview.bin.Cache.getProperty("VERSION") + + "_" + + jalview.bin.Cache.getDefault("BUILD_DATE", + "unknown")), "UA-9060947-1" }); + jgoogleanalyticstracker.getMethod("trackAsynchronously", + new Class[] + { trackerfocus }).invoke(tracker, new Object[] + { trackerfocus.getConstructor(new Class[] + { String.class }).newInstance(new Object[] + { "Application Started." }) }); + } catch (RuntimeException e) + { + re = e; + } catch (Exception e) + { + ex = e; + } catch (Error e) + { + err = e; + } + if (re != null || ex != null || err != null) + { + if (log != null) + { + if (re != null) + log.debug("Caught runtime exception in googletracker init:", re); + if (ex != null) + log.warn( + "Failed to initialise GoogleTracker for Jalview Desktop with version " + + vrs, ex); + if (err != null) + log.error( + "Whilst initing GoogleTracker for Jalview Desktop version " + + vrs, err); + } + else + { + if (re != null) + { + System.err + .println("Debug: Caught runtime exception in googletracker init:" + + vrs); + re.printStackTrace(); + } + if (ex != null) + { + System.err + .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version " + + vrs); + ex.printStackTrace(); + } + + if (err != null) + { + System.err + .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version " + + vrs); + err.printStackTrace(); } - } catch (Exception e) { - vamsasJarsArePresent=0; - jalview.bin.Cache.log.debug("Vamsas Classes are not present"); } } - return (vamsasJarsArePresent>0); + else + { + log.debug("Successfully initialised tracker."); + } + } + } + + /** + * get the user's default colour if available + * @param property + * @param defcolour + * @return + */ + public static Color getDefaultColour(String property, Color defcolour) + { + String colprop = getProperty(property); + if (colprop==null) { + return defcolour; } + Color col = jalview.schemes.ColourSchemeProperty.getAWTColorFromName(colprop); + if (col==null) + { + try { + col = new jalview.schemes.UserColourScheme(colprop).findColour('A'); + } catch (Exception ex) + { + log.warn("Couldn't parse '"+colprop+"' as a colour for "+property); + col=null; + } + } + return (col==null) ? defcolour: col; + } + + /** + * store a colour as a Jalview user default property + * @param property + * @param colour + */ + public static void setColourProperty(String property, Color colour) + { + setProperty(property, jalview.util.Format + .getHexString(colour)); + } + + public static final DateFormat date_format = SimpleDateFormat.getDateTimeInstance(); + /** + * store a date in a jalview property + * @param string + * @param time + */ + public static void setDateProperty(String property, Date time) + { + setProperty(property, date_format.format(time)); + } + /** + * read a date stored in a jalview property + * @param property + * @return valid date as stored by setDateProperty, or null + * + */ + public static Date getDateProperty(String property) + { + String val = getProperty(property); + if (val!=null) + { + try { + return date_format.parse(val); + } catch (Exception ex) + { + System.err.println("Invalid or corrupt date in property '"+property+"' : value was '"+val+"'"); + } + } + return null; + } }