X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=ab0814070c48bb0c8fa52e0eff7bdddc9a25454c;hb=e1aa3fdd1ca82abf5acc0cd3c2b86a5ca1083941;hp=1b5ba56e70a5ce72899e98fd195b731dc04d4dc6;hpb=a91379944accf50c8dc0082c61e399dffbd7287a;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 1b5ba56..2904fc3 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,329 +1,1229 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * 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. - * - * 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.bin; -import java.io.*; +import java.awt.Color; +import java.io.BufferedReader; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileOutputStream; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.PrintWriter; +import java.io.StringWriter; +import java.text.DateFormat; +import java.text.SimpleDateFormat; +import java.util.Collections; +import java.util.Date; +import java.util.Enumeration; +import java.util.Locale; +import java.util.Properties; +import java.util.StringTokenizer; +import java.util.TreeSet; +import java.util.regex.Pattern; -import java.util.*; +import javax.swing.LookAndFeel; +import javax.swing.UIManager; +import org.apache.log4j.ConsoleAppender; +import org.apache.log4j.Level; import org.apache.log4j.Logger; import org.apache.log4j.SimpleLayout; -import org.apache.log4j.Level; -import org.apache.log4j.ConsoleAppender; +import jalview.datamodel.PDBEntry; +import jalview.gui.UserDefinedColours; +import jalview.schemes.ColourSchemeLoader; +import jalview.schemes.ColourSchemes; +import jalview.schemes.UserColourScheme; +import jalview.structure.StructureImportSettings; +import jalview.urls.IdOrgSettings; +import jalview.util.ColorUtils; +import jalview.ws.sifts.SiftsSettings; /** - * 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"; + + /** + * Sifts settings + */ + public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System + .getProperty("user.home") + File.separatorChar + + ".sifts_downloads" + File.separatorChar; + + private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2"; + + private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30"; + + /** + * Identifiers.org download settings + */ + private static final String ID_ORG_FILE = System.getProperty("user.home") + + File.separatorChar + ".identifiers.org.ids.json"; + + /** + * Allowed values are PDB or mmCIF + */ + private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF + .toString(); + + private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER + .toString(); + + /* + * a date formatter using a fixed (rather than the user's) locale; + * this ensures that date properties can be written and re-read successfully + * even if the user changes their locale setting + */ + private static final DateFormat date_format = SimpleDateFormat + .getDateTimeInstance(SimpleDateFormat.MEDIUM, + SimpleDateFormat.MEDIUM, Locale.UK); + + /** + * 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() + { + // override results in properties output in alphabetical order + @Override + public synchronized Enumeration keys() + { + return Collections.enumeration(new TreeSet<>(super.keySet())); + } + }; + + /** 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"); - /** Default file is ~/.jalview_properties */ - static String propertiesFile; + 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()))); + // we shouldn't need to do this + org.apache.log4j.Logger.getRootLogger() + .setLevel(org.apache.log4j.Level.INFO); - public static void initLogger() + 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); + } + } + + /** + * Loads properties from the given properties file. Any existing properties + * are first cleared. + */ + 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; + } + + 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.clear(); + applicationProperties.load(fis); + + // remove any old build properties + + deleteBuildProperties(); + fis.close(); + } catch (Exception ex) + { + System.out.println("Error reading properties file: " + ex); } + if (getDefault("USE_PROXY", false)) + { + String proxyServer = getDefault("PROXY_SERVER", ""), + proxyPort = getDefault("PROXY_PORT", "8080"); + + System.out.println("Using proxyServer: " + proxyServer + + " proxyPort: " + proxyPort); + + System.setProperty("http.proxyHost", proxyServer); + System.setProperty("http.proxyPort", proxyPort); + } - /** 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"); - } + loadBuildProperties(false); - String jnlpVersion = System.getProperty("jalview.version"); - String codeVersion = getProperty("VERSION"); + SiftsSettings + .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false)); + SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache + .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR)); - if(codeVersion==null) - { - // THIS SHOULD ONLY BE THE CASE WHEN TESTING!! - codeVersion = "Test"; - jnlpVersion = "Test"; - } + SiftsSettings.setFailSafePIDThreshold( + jalview.bin.Cache.getDefault("sifts_fail_safe_pid_threshold", + DEFAULT_FAIL_SAFE_PID_THRESHOLD)); + + SiftsSettings.setCacheThresholdInDays( + jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days", + DEFAULT_CACHE_THRESHOLD_IN_DAYS)); + IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL", + "https://www.jalview.org/services/identifiers")); + IdOrgSettings.setDownloadLocation(ID_ORG_FILE); - System.out.println("Jalview Version: "+codeVersion); + StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache + .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT)); + StructureImportSettings + .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER); + // StructureImportSettings + // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault( + // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER)); + String jnlpVersion = System.getProperty("jalview.version"); - // 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"))) + // jnlpVersion will be null if a latest version check for the channel needs + // to be done + // 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"))) + { + + class VersionChecker extends Thread + { + + @Override + public void run() { + String buildPropertiesUrl = Cache.getAppbaseBuildProperties(); - class VersionChecker - extends Thread + String orgtimeout = System + .getProperty("sun.net.client.defaultConnectTimeout"); + if (orgtimeout == null) { - public void run() - { - 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) - { - System.out.println(ex); - jnlpVersion = getProperty("VERSION"); - } - - setProperty("LATEST_VERSION", jnlpVersion); - } + orgtimeout = "30"; + System.out.println("# INFO: Setting default net timeout to " + + orgtimeout + " seconds."); } + String remoteVersion = null; + try + { + System.setProperty("sun.net.client.defaultConnectTimeout", + "5000"); + java.net.URL url = new java.net.URL(buildPropertiesUrl); - VersionChecker vc = new VersionChecker(); - vc.start(); - } - else - { - if(jnlpVersion!=null) - setProperty("LATEST_VERSION", jnlpVersion); - else - applicationProperties.remove("LATEST_VERSION"); - } + BufferedReader in = new BufferedReader( + new InputStreamReader(url.openStream())); - setProperty("VERSION", codeVersion); + Properties remoteBuildProperties = new Properties(); + remoteBuildProperties.load(in); + remoteVersion = remoteBuildProperties.getProperty("VERSION"); + } catch (Exception ex) + { + System.out + .println("Non-fatal exception when checking version at " + + buildPropertiesUrl + ":"); + System.out.println(ex); + remoteVersion = getProperty("VERSION"); + } + System.setProperty("sun.net.client.defaultConnectTimeout", + orgtimeout); - //LOAD USERDEFINED COLOURS - jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS")); - jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false); + setProperty("LATEST_VERSION", remoteVersion); + } + } + + VersionChecker vc = new VersionChecker(); + vc.start(); + } + else + { + if (jnlpVersion != null) + { + setProperty("LATEST_VERSION", jnlpVersion); + } + else + { + applicationProperties.remove("LATEST_VERSION"); + } } + // LOAD USERDEFINED COLOURS + jalview.bin.Cache + .initUserColourSchemes(getProperty("USER_DEFINED_COLOURS")); + jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", + false); + } + public static void loadBuildProperties(boolean reportVersion) + { + String codeInstallation = getProperty("INSTALLATION"); + boolean printV = codeInstallation == null; + + // FIND THE VERSION NUMBER AND BUILD DATE FROM jalview.jar + 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"); + } + String codeVersion = getProperty("VERSION"); + codeInstallation = getProperty("INSTALLATION"); - /** - * 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) + if (codeVersion == null) { - return applicationProperties.getProperty(key); + // THIS SHOULD ONLY BE THE CASE WHEN TESTING!! + codeVersion = "Test"; + codeInstallation = ""; } + else + { + codeInstallation = " (" + codeInstallation + ")"; + } + setProperty("VERSION", codeVersion); + new BuildDetails(codeVersion, null, codeInstallation); + if (printV && reportVersion) + { + System.out.println( + "Jalview Version: " + codeVersion + codeInstallation); + } + } + + private static void deleteBuildProperties() + { + applicationProperties.remove("LATEST_VERSION"); + applicationProperties.remove("VERSION"); + applicationProperties.remove("AUTHORS"); + applicationProperties.remove("AUTHORFNAMES"); + applicationProperties.remove("YEAR"); + applicationProperties.remove("BUILD_DATE"); + applicationProperties.remove("INSTALLATION"); + } + + /** + * 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(); + } - /** These methods are used when checking if the saved preference - * is different to the default setting - */ + return def; + } - public static boolean getDefault(String property, boolean def) + public static int getDefault(String property, int def) + { + String string = getProperty(property); + if (string != null) { - String string = getProperty(property); - if (string != null) + try { - def = Boolean.valueOf(string).booleanValue(); + def = Integer.parseInt(string); + } catch (NumberFormatException e) + { + System.out.println("Error parsing int property '" + property + + "' with value '" + string + "'"); } + } - return def; + return def; + } + + /** + * 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 string; } - /** These methods are used when checking if the saved preference - * is different to the default setting - */ - public static String getDefault(String property, String def) + return def; + } + + /** + * Stores property in the file "HOME_DIR/.jalview_properties" + * + * @param key + * Name of object + * @param obj + * String value of property + * + * @return previous value of property (or null) + */ + public static Object setProperty(String key, String obj) + { + Object oldValue = null; + try { - String string = getProperty(property); - if (string != null) + oldValue = applicationProperties.setProperty(key, obj); + if (propertiesFile != null && !propsAreReadOnly) { - return string; + FileOutputStream out = new FileOutputStream(propertiesFile); + applicationProperties.store(out, "---JalviewX Properties File---"); + out.close(); } + } catch (Exception ex) + { + System.out.println( + "Error setting property: " + key + " " + obj + "\n" + ex); + } + return oldValue; + } + + /** + * remove the specified property from the jalview properties file + * + * @param string + */ + public static void removeProperty(String string) + { + applicationProperties.remove(string); + saveProperties(); + } - return def; + /** + * save the properties to the jalview properties path + */ + public static void saveProperties() + { + if (!propsAreReadOnly) + { + try + { + FileOutputStream out = new FileOutputStream(propertiesFile); + applicationProperties.store(out, "---JalviewX Properties File---"); + out.close(); + } catch (Exception ex) + { + System.out.println("Error saving properties: " + ex); + } } + } + /** + * internal vamsas class discovery state + */ + private static int vamsasJarsArePresent = -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 vamsasJarsPresent() + { + if (vamsasJarsArePresent == -1) { - try + try + { + if (jalview.jbgui.GDesktop.class.getClassLoader() + .loadClass("uk.ac.vamsas.client.VorbaId") != null) { - FileOutputStream out = new FileOutputStream(propertiesFile); - applicationProperties.setProperty(key, obj); - applicationProperties.store(out, "---JalviewX Properties File---"); - out.close(); + 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 ex) - { System.out.println("Error setting property: "+key+" "+obj+"\n"+ex); } - return obj; + } catch (Exception e) + { + vamsasJarsArePresent = 0; + jalview.bin.Cache.log.debug("Vamsas Classes are not present"); + } } + return (vamsasJarsArePresent > 0); + } - public static void saveProperties() + /** + * internal vamsas class discovery state + */ + private static int groovyJarsArePresent = -1; + + /** + * 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 + { + if (Cache.class.getClassLoader() + .loadClass("groovy.lang.GroovyObject") != null) + { + 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 (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); + } + + /** + * 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 { - FileOutputStream out = new FileOutputStream(propertiesFile); - applicationProperties.store(out, "---JalviewX Properties File---"); - out.close(); + 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 ex) - { System.out.println("Error saving properties: "+ex); } - } - /** - * 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."); + } + 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 = ColorUtils.parseColourString(colprop); + if (col == null) + { + log.warn("Couldn't parse '" + colprop + "' as a colour for " + + property); + } + 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)); + } + + /** + * Stores a formatted date in a jalview property, using a fixed locale. + * + * @param propertyName + * @param date + * @return the formatted date string + */ + public static String setDateProperty(String propertyName, Date date) + { + String formatted = date_format.format(date); + setProperty(propertyName, formatted); + return formatted; + } + + /** + * Reads a date stored in a Jalview property, parses it (using a fixed locale + * format) and returns as a Date, or null if parsing fails + * + * @param propertyName + * @return + * + */ + public static Date getDateProperty(String propertyName) + { + String val = getProperty(propertyName); + if (val != null) + { + try + { + return date_format.parse(val); + } catch (Exception ex) + { + System.err.println("Invalid or corrupt date in property '" + + propertyName + "' : value was '" + val + "'"); + } + } + return null; + } + + /** + * get and parse a property as an integer. send any parsing problems to + * System.err + * + * @param property + * @return null or Integer + */ + public static Integer getIntegerProperty(String property) + { + String val = getProperty(property); + if (val != null && (val = val.trim()).length() > 0) + { + try + { + return Integer.valueOf(val); + } catch (NumberFormatException x) + { + System.err.println("Invalid integer in property '" + property + + "' (value was '" + val + "')"); + } + } + return null; + } + + /** + * Set the specified value, or remove it if null or empty. Does not save the + * properties file. + * + * @param propName + * @param value + */ + public static void setOrRemove(String propName, String value) + { + if (propName == null) + { + return; + } + if (value == null || value.trim().length() < 1) + { + Cache.applicationProperties.remove(propName); + } + else + { + Cache.applicationProperties.setProperty(propName, value); + } + } + + /** + * Loads in user colour schemes from files. + * + * @param files + * a '|'-delimited list of file paths + */ + public static void initUserColourSchemes(String files) + { + if (files == null || files.length() == 0) + { + return; + } + + // In case colours can't be loaded, we'll remove them + // from the default list here. + StringBuffer coloursFound = new StringBuffer(); + StringTokenizer st = new StringTokenizer(files, "|"); + while (st.hasMoreElements()) + { + String file = st.nextToken(); + try + { + UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file); + if (ucs != null) + { + if (coloursFound.length() > 0) + { + coloursFound.append("|"); } - } catch (Exception e) { - vamsasJarsArePresent=0; - jalview.bin.Cache.log.debug("Vamsas Classes are not present"); + coloursFound.append(file); + ColourSchemes.getInstance().registerColourScheme(ucs); } + } catch (Exception ex) + { + System.out.println("Error loading User ColourFile\n" + ex); + } + } + if (!files.equals(coloursFound.toString())) + { + if (coloursFound.toString().length() > 1) + { + setProperty(UserDefinedColours.USER_DEFINED_COLOURS, + coloursFound.toString()); + } + else + { + applicationProperties + .remove(UserDefinedColours.USER_DEFINED_COLOURS); } - return (vamsasJarsArePresent>0); } + } + + /** + * Initial logging information helper for various versions output + * + * @param prefix + * @param value + * @param defaultValue + */ + private static void appendIfNotNull(StringBuilder sb, String prefix, + String value, String suffix, String defaultValue) + { + if (value == null && defaultValue == null) + { + return; + } + String line = prefix + (value != null ? value : defaultValue) + suffix; + sb.append(line); + } + + /** + * + * @return Jalview version, build details and JVM platform version for console + */ + public static String getVersionDetailsForConsole() + { + StringBuilder sb = new StringBuilder(); + sb.append("Jalview Version: "); + sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST")); + sb.append("\n"); + sb.append("Jalview Installation: "); + sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown")); + sb.append("\n"); + sb.append("Build Date: "); + sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")); + sb.append("\n"); + sb.append("Java version: "); + sb.append(System.getProperty("java.version")); + sb.append("\n"); + sb.append(System.getProperty("os.arch")); + sb.append(" "); + sb.append(System.getProperty("os.name")); + sb.append(" "); + sb.append(System.getProperty("os.version")); + sb.append("\n"); + appendIfNotNull(sb, "Install4j version: ", + System.getProperty("sys.install4jVersion"), "\n", null); + appendIfNotNull(sb, "Install4j template version: ", + System.getProperty("installer_template_version"), "\n", null); + appendIfNotNull(sb, "Launcher version: ", + System.getProperty("launcher_version"), "\n", null); + LookAndFeel laf = UIManager.getLookAndFeel(); + String lafName = laf == null ? "Not obtained" : laf.getName(); + String lafClass = laf == null ? "unknown" : laf.getClass().getName(); + sb.append("LookAndFeel: "); + sb.append(lafName); + sb.append(" ("); + sb.append(lafClass); + sb.append(")\n"); + // Not displayed in release version ( determined by possible version number + // regex 9[9.]*9[.-_a9]* ) + if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$", + jalview.bin.Cache.getDefault("VERSION", "TEST"))) + { + appendIfNotNull(sb, "Getdown appdir: ", + System.getProperty("getdownappdir"), "\n", null); + appendIfNotNull(sb, "Getdown appbase: ", + System.getProperty("getdownappbase"), "\n", null); + appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"), + "\n", "unknown"); + } + return sb.toString(); + } + + /** + * + * @return build details as reported in splashscreen + */ + public static String getBuildDetailsForSplash() + { + // consider returning more human friendly info + // eg 'built from Source' or update channel + return jalview.bin.Cache.getDefault("INSTALLATION", "unknown"); + } + + public static String getStackTraceString(Throwable t) + { + StringWriter sw = new StringWriter(); + PrintWriter pw = new PrintWriter(sw); + t.printStackTrace(pw); + return sw.toString(); + } + + /** + * Getdown appbase methods + */ + + private static final String releaseAppbase; + + private static String getdownAppbase; + + private static String getdownDistDir; + + static + { + Float specversion = Float + .parseFloat(System.getProperty("java.specification.version")); + releaseAppbase = (specversion < 9) + ? "https://www.jalview.org/getdown/release/1.8" + : "https://www.jalview.org/getdown/release/11"; + } + + // look for properties (passed in by getdown) otherwise default to release + private static void setGetdownAppbase() + { + if (getdownAppbase != null) + { + return; + } + String appbase = System.getProperty("getdownappbase"); + String distDir = System.getProperty("getdowndistdir"); + if (appbase == null) + { + appbase = releaseAppbase; + distDir = "release"; + } + if (appbase.endsWith("/")) + { + appbase = appbase.substring(0, appbase.length() - 1); + } + if (distDir == null) + { + distDir = appbase.equals(releaseAppbase) ? "release" : "alt"; + } + getdownAppbase = appbase; + getdownDistDir = distDir; + } + + public static String getGetdownAppbase() + { + setGetdownAppbase(); + return getdownAppbase; + } + public static String getAppbaseBuildProperties() + { + String appbase = getGetdownAppbase(); + return appbase + "/" + getdownDistDir + "/build_properties"; + } }