X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=acf1499a15bb742510664932f9046558773d547f;hb=87185978c81d7d07f683f0c1a1bac5f080e88192;hp=1050a568bcb0110a73af44d69ab2162048d0ad96;hpb=e61219eaa31557203fa518aa03cba2cc651e1b84;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 1050a56..acf1499 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 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 @@ -19,27 +19,75 @@ package jalview.bin; import java.io.*; - 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.*; /** * 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: + * * @author $author$ * @version $Revision$ @@ -47,275 +95,352 @@ import org.apache.log4j.ConsoleAppender; 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.Castor.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"; + + /** + * 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; + /** Default file is ~/.jalview_properties */ + static String propertiesFile; - public static void initLogger() + public static void initLogger() + { + try + { + 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()))); + 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) { - 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."); - } - catch (Exception ex) - { System.err.println("Problems initializing the log4j system\n"); - } + ex.printStackTrace(System.err); } + } - - /** Called when Jalview is started */ - public static void loadProperties(String propsFile) + /** Called when Jalview is started */ + public static void loadProperties(String propsFile) + { + propertiesFile = propsFile; + if (propsFile == null) { - propertiesFile = propsFile; - if (propsFile == null) - { - propertiesFile = System.getProperty("user.home") + "/.jalview_properties"; - } - - 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); - } - - 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)); - } + propertiesFile = System.getProperty("user.home") + File.separatorChar + + ".jalview_properties"; + } - // 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"); - } + 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); + } - String jnlpVersion = System.getProperty("jalview.version"); - String codeVersion = getProperty("VERSION"); + 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)); + } + // 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"); + } - 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 && ( + 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 jnlpVersion = null; + try { - public void run() + 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) { - 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("\"")); + jnlpVersion = line; + break; } } + catch (Exception ex) + { + System.out.println(ex); + jnlpVersion = getProperty("VERSION"); + } - 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 + */ - /** - * 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) + public static boolean getDefault(String property, boolean def) + { + String string = getProperty(property); + if (string != null) { - return applicationProperties.getProperty(key); + def = Boolean.valueOf(string).booleanValue(); } + return def; + } - /** These methods are used when checking if the saved preference - * is different to the default setting - */ - - public static boolean getDefault(String property, boolean 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) { - String string = getProperty(property); - if (string != null) - { - def = Boolean.valueOf(string).booleanValue(); - } - - return def; + 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) - { - String string = getProperty(property); - if (string != null) - { - return string; - } + return def; + } - return def; + /** + * 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) + { + try + { + FileOutputStream out = new FileOutputStream(propertiesFile); + applicationProperties.setProperty(key, obj); + applicationProperties.store(out, "---JalviewX Properties File---"); + out.close(); } + catch (Exception ex) + { + System.out.println("Error setting property: " + key + " " + obj + "\n" + + ex); + } + return obj; + } - - /** - * 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 void saveProperties() + { + try { - try - { - FileOutputStream out = new FileOutputStream(propertiesFile); - applicationProperties.setProperty(key, obj); - applicationProperties.store(out, "---JalviewX Properties File---"); - out.close(); - } - catch (Exception ex) - { System.out.println("Error setting property: "+key+" "+obj+"\n"+ex); } - return obj; + FileOutputStream out = new FileOutputStream(propertiesFile); + applicationProperties.store(out, "---JalviewX Properties File---"); + out.close(); } + catch (Exception ex) + { + System.out.println("Error saving properties: " + ex); + } + } - public static void saveProperties() + /** + * 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 + try + { + if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass( + "uk.ac.vamsas.client.VorbaId") != null) { - FileOutputStream out = new FileOutputStream(propertiesFile); - 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 saving properties: "+ex); } + } + catch (Exception e) + { + vamsasJarsArePresent = 0; + jalview.bin.Cache.log.debug("Vamsas Classes are not present"); + } } - /** - * 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; - } - } 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; + /** + * 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."); } } - return (vamsasJarsArePresent>0); + catch (Exception e) + { + groovyJarsArePresent = 0; + jalview.bin.Cache.log.debug("Groovy Classes are not present"); + } } + return (groovyJarsArePresent > 0); + } }