X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=b24304af8e1cebef630a7919ba7e2b03aca088b1;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=0927272098a14d2ae8117342ba75c37477bc2fa8;hpb=483d42f1582a50546525aeacb2b298a7c3d87d09;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 0927272..b15c317 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,328 +1,1186 @@ /* - * 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 jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; +import jalview.datamodel.PDBEntry; +import jalview.gui.Preferences; +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.util.Platform; +import jalview.ws.sifts.SiftsSettings; -import java.util.*; +import java.awt.Color; +import java.awt.Dimension; +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.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 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; - /** - * 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 +public class Cache implements ApplicationSingletonI { + + private Cache() + { + // private singleton + } + + /** + * In Java, this will be a static field instance, which will be + * application-specific; in JavaScript it will be an applet-specific instance + * tied to the applet's ThreadGroup. + * + * @return + */ + private static Cache getInstance() + { + return (Cache) ApplicationSingletonProvider.getInstance(Cache.class); + } + + /** + * 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"; + /** - * Initialises the Apache Axis logger + * 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 */ + // BH 2019.05.08 was static + @SuppressWarnings("serial") + private 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; + /** Default file is ~/.jalview_properties */ + private String propertiesFile; - public static void initLogger() + /** + * flag to possibly allow properties to be written to a property file + */ + private boolean propsAreReadOnly = Platform.isJS(); + + private final static String JS_PROPERTY_PREFIX = "jalview_"; + + public static void initLogger() + { + if (log != null) { - try + 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( + getDefault("logs.Axis.Level", Level.INFO.toString()))); + lcastor.setLevel(Level.toLevel( + getDefault("logs.Castor.Level", Level.INFO.toString()))); + lcastor = Logger.getLogger("org.exolab.castor.xml"); + lcastor.setLevel(Level.toLevel( + getDefault("logs.Castor.Level", Level.INFO.toString()))); + // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller"); + // lcastor.setLevel(Level.toLevel(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); + } + } + + /** + * Loads properties from the given properties file. Any existing properties + * are first cleared. + */ + public static void loadProperties(String propsFile) + { + getInstance().loadPropertiesImpl(propsFile); + } + + private void loadPropertiesImpl(String propsFile) + { + propertiesFile = propsFile; + if (!propsAreReadOnly) + { + // Java only + if (propsFile == null) { - 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."); + propertiesFile = System.getProperty("user.home") + + File.separatorChar + ".jalview_properties"; } - catch (Exception ex) + else { - System.err.println("Problems initializing the log4j system\n"); + // don't corrupt the file we've been given. + propsAreReadOnly = true; } } - - /** Called when Jalview is started */ - public static void loadProperties(String propsFile) + if (propertiesFile == null) + { // BH 2019 read properties from the Info object associated with this + // applet + Platform.readInfoProperties(JS_PROPERTY_PREFIX, + applicationProperties); + } + else { - propertiesFile = propsFile; - if (propsFile == null) + try + { + InputStream fis; + try { - propertiesFile = System.getProperty("user.home") +File.separatorChar+".jalview_properties"; - } + 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; - try + } catch (Exception ex) { - FileInputStream fis = new FileInputStream(propertiesFile); - applicationProperties.load(fis); - applicationProperties.remove("LATEST_VERSION"); - applicationProperties.remove("VERSION"); - fis.close(); + fis = null; } - catch (Exception ex) + if (fis == null) { - System.out.println("Error reading properties file: "+ex); + fis = new FileInputStream(propertiesFile); } + applicationProperties.clear(); + applicationProperties.load(fis); - if(getDefault("USE_PROXY", false)) + // remove any old build properties + + deleteBuildProperties(); + fis.close(); + } catch (Exception ex) { - 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)); + System.out.println("Error reading properties file: " + ex); } + } + if (getDefault("USE_PROXY", false)) + { + String proxyServer = getDefault("PROXY_SERVER", ""), + proxyPort = getDefault("PROXY_PORT", "8080"); - // 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"); - } + System.out.println("Using proxyServer: " + proxyServer + + " proxyPort: " + proxyPort); - String jnlpVersion = System.getProperty("jalview.version"); - String codeVersion = getProperty("VERSION"); + System.setProperty("http.proxyHost", proxyServer); + System.setProperty("http.proxyPort", proxyPort); + } + // LOAD THE AUTHORS FROM THE authors.props file + String authorDetails = (Platform.isJS() ? null + : "jar:".concat(Cache.class.getProtectionDomain() + .getCodeSource().getLocation().toString() + .concat("!/authors.props"))); - if(codeVersion==null) - { - // THIS SHOULD ONLY BE THE CASE WHEN TESTING!! - codeVersion = "Test"; - jnlpVersion = "Test"; - } + try + { + if (authorDetails != null) + { + java.net.URL localJarFileURL = new java.net.URL(authorDetails); + InputStream in = localJarFileURL.openStream(); + applicationProperties.load(in); + in.close(); + } + } catch (Exception ex) + { + System.out.println("Error reading author details: " + ex); + authorDetails = null; + } + if (authorDetails == null) + { + 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 + String buildDetails = (Platform.isJS() ? null + : "jar:".concat(Cache.class.getProtectionDomain() + .getCodeSource().getLocation().toString() + .concat("!/.build_properties"))); + if (buildDetails != null) + { + try + { + 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); + buildDetails = null; + } + } + if (buildDetails == null) + { + applicationProperties.remove("VERSION"); + } + String jnlpVersion = System.getProperty("jalview.version"); + String codeVersion = getProperty("VERSION"); + String codeInstallation = getProperty("INSTALLATION"); + if (codeVersion == null) + { + // THIS SHOULD ONLY BE THE CASE WHEN TESTING!! + codeVersion = "Test"; + jnlpVersion = "Test"; + codeInstallation = ""; + } + else + { + codeInstallation = " (" + codeInstallation + ")"; + } + new BuildDetails(codeVersion, null, codeInstallation); + SiftsSettings.setMapWithSifts(getDefault("MAP_WITH_SIFTS", false)); - System.out.println("Jalview Version: "+codeVersion); + SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache + .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR)); + SiftsSettings.setFailSafePIDThreshold( + getDefault("sifts_fail_safe_pid_threshold", + DEFAULT_FAIL_SAFE_PID_THRESHOLD)); - // 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"))) - { + SiftsSettings.setCacheThresholdInDays( + getDefault("sifts_cache_threshold_in_days", + DEFAULT_CACHE_THRESHOLD_IN_DAYS)); - class VersionChecker - extends Thread + IdOrgSettings.setUrl(getDefault(Preferences.ID_ORG_HOSTURL, + "http://www.jalview.org/services/identifiers")); + IdOrgSettings.setDownloadLocation(ID_ORG_FILE); + + System.out + .println("Jalview Version: " + codeVersion + codeInstallation); + + StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache + .getDefault(Preferences.PDB_DOWNLOAD_FORMAT, PDB_DOWNLOAD_FORMAT)); + StructureImportSettings + .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER); + // StructureImportSettings + // .setDefaultPDBFileParser(jalview.bin.getDefault( + // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER)); + // jnlpVersion will be null if we're using InstallAnywhere + // Dont do this check if running in headless mode + if (jnlpVersion == null && !Jalview.isHeadlessMode() + && getDefault("VERSION_CHECK", true)) + { + + class VersionChecker extends Thread + { + @Override + public void run() + { + 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 remoteVersion = 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 + if (line.indexOf("jalview.version") == -1) { - 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"); + continue; } - setProperty("LATEST_VERSION", jnlpVersion); + line = line.substring(line.indexOf("value=") + 7); + line = line.substring(0, line.lastIndexOf("\"")); + remoteVersion = line; + break; } + } catch (Exception ex) + { + System.out.println( + "Non-fatal exception when checking version at www.jalview.org :"); + System.out.println(ex); + remoteVersion = 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", remoteVersion); } + } + + 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 + initUserColourSchemes(getProperty(Preferences.USER_DEFINED_COLOURS)); + } + + private 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"); + } - setProperty("VERSION", codeVersion); + /** + * 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 getInstance().applicationProperties.getProperty(key); + } + + /** + * These methods are used when checking if the saved preference is different + * to the default setting + */ - //LOAD USERDEFINED COLOURS - jalview.gui.UserDefinedColours.initUserColourSchemes( getProperty("USER_DEFINED_COLOURS")); - jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER", false); + public static boolean getDefault(String property, boolean def) + { + String string = getProperty(property); + if (string != null) + { + def = Boolean.valueOf(string).booleanValue(); } + return def; + } + public static int getDefault(String property, int def) + { + String string = getProperty(property); + if (string != null) + { + try + { + def = Integer.parseInt(string); + } catch (NumberFormatException e) + { + System.out.println("Error parsing int property '" + property + + "' with value '" + string + "'"); + } + } - /** - * 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 def; + } + + /** + * retrieve a dimension, such as for Jmol + * + * @param property + * @param def + * @return + */ + public static Dimension getDefaultDim(String property, Dimension def) + { + String s = getProperty(property); + if (s != null) { - return applicationProperties.getProperty(key); + if (s.indexOf(',') < 0) + { + s = s.trim().replace(' ', ','); + if (s.indexOf(',') < 0) + { + s += "," + s; + } + } + try + { + int pt = s.indexOf(","); + return new Dimension(Integer.parseInt(s.substring(0, pt)), + Integer.parseInt(s.substring(pt + 1))); + } catch (NumberFormatException e) + { + System.out.println("Error parsing Dimension property '" + property + + "' with value '" + s + "'"); + } } + return def; + } + + /** + * Answers the value of the given property, or the supplied default value if + * the property is not set + */ + public static String getDefault(String property, String def) + { + String value = getProperty(property); + return value == null ? def : value; + } + /** + * 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) + { + return getInstance().setPropertyImpl(key, obj, true); + } - /** These methods are used when checking if the saved preference - * is different to the default setting - */ + public static void setPropertyNoSave(String key, String obj) + { + getInstance().setPropertyImpl(key, obj, false); + } - public static boolean getDefault(String property, boolean def) + private Object setPropertyImpl(String key, String obj, boolean andSave) + { + Object oldValue = null; + try { - String string = getProperty(property); - if (string != null) + oldValue = applicationProperties.setProperty(key, obj); + if (andSave && !propsAreReadOnly && propertiesFile != null) { - def = Boolean.valueOf(string).booleanValue(); + 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; + } - return def; + /** + * remove the specified property from the jalview properties file + * + * @param key + */ + public static void removeProperty(String key) + { + getInstance().removePropertyImpl(key, true); + } + + public static void removePropertyNoSave(String key) + { + getInstance().removePropertyImpl(key, false); + } + + private void removePropertyImpl(String key, boolean andSave) + { + applicationProperties.remove(key); + if (andSave) + { + savePropertiesImpl(); } + } - /** These methods are used when checking if the saved preference - * is different to the default setting - */ - public static String getDefault(String property, String def) + public static void saveProperties() + { + getInstance().savePropertiesImpl(); + } + + /** + * save the properties to the jalview properties path + */ + private void savePropertiesImpl() + { + 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); } + } + } + + private final static int UNTESTED = -1; + + private final static int TRUE = 1; + + private final static int FALSE = 0; - return def; + /** + * internal vamsas class discovery state + */ + private static int vamsasJarsArePresent = (Platform.isJS() ? FALSE + : UNTESTED); + + /** + * Searches for vamsas client classes on class path. + * + * @return true if vamsas client is present on classpath + */ + public static boolean vamsasJarsPresent() + { + if (vamsasJarsArePresent == UNTESTED) + { + 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 = TRUE; + 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 = FALSE; + jalview.bin.Cache.log.debug("Vamsas Classes are not present"); + } } + return (vamsasJarsArePresent == TRUE); + } + /** + * internal vamsas class discovery state + */ + private static int groovyJarsArePresent = (Platform.isJS() ? FALSE + : UNTESTED); - /** - * 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 == UNTESTED) { - 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 = TRUE; + 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 = FALSE; + jalview.bin.Cache.log.debug("Groovy Classes are not present", e); + } catch (Exception e) + { + groovyJarsArePresent = FALSE; + jalview.bin.Cache.log.debug("Groovy Classes are not present"); + } } + return (groovyJarsArePresent == TRUE); + } + + /** + * GA tracker object - actually JGoogleAnalyticsTracker null if tracking not + * enabled. + */ + protected static Object tracker = null; - public static void saveProperties() + protected static Class trackerfocus = null; + + protected static Class jgoogleanalyticstracker = null; + + /** + * Initialise the google tracker if it is not done already. + */ + public static void initGoogleTracker() + { + + // TODO: SwingJS JavaScript tracker? + + 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; } - 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("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."); + } + // 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") + "_" + + 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); } - } catch (Exception e) { - vamsasJarsArePresent=0; - jalview.bin.Cache.log.debug("Vamsas Classes are not present"); } + 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(); + } + } + } + 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) + { + getInstance().applicationProperties.remove(propName); + } + else + { + getInstance().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("|"); + } + 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(Preferences.USER_DEFINED_COLOURS, + coloursFound.toString()); + } + else + { + getInstance().applicationProperties + .remove(Preferences.USER_DEFINED_COLOURS); } - return (vamsasJarsArePresent>0); } + } }