X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=a43714ffb4948de6b3e6130137032401bea7cf1b;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=9702a9231b54e9976e54ef77130d8ef0fa8007c5;hpb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 9702a92..a43714f 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,297 +1,298 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 - */ -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; - - -/** - * 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 - - * @author $author$ - * @version $Revision$ - */ -public class Cache -{ - /** - * Initialises the Apache Axis logger - */ - public static Logger log; - - /** Jalview Properties */ - public static Properties applicationProperties = new Properties(); - - /** Default file is ~/.jalview_properties */ - static String propertiesFile; - - public static void initLogger() - { - 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"); - } - } - - - /** Called when Jalview is started */ - public static void loadProperties(String propsFile) - { - 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)); - } - - // 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"); - } - - 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); - - - // 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() - { - 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); - } - } - - 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")); - } - - - - /** - * 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; - } - - /** 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; - } - - - /** - * 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; - } - - public static void saveProperties() - { - try - { - FileOutputStream out = new FileOutputStream(propertiesFile); - applicationProperties.store(out, "---JalviewX Properties File---"); - out.close(); - } - catch (Exception ex) - { System.out.println("Error saving properties: "+ex); } - } -} +/* + * 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 + */ +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; + + +/** + * 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 + + * @author $author$ + * @version $Revision$ + */ +public class Cache +{ + /** + * Initialises the Apache Axis logger + */ + public static Logger log; + + /** Jalview Properties */ + public static Properties applicationProperties = new Properties(); + + /** Default file is ~/.jalview_properties */ + static String propertiesFile; + + public static void initLogger() + { + 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"); + } + } + + + /** Called when Jalview is started */ + public static void loadProperties(String propsFile) + { + 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)); + } + + // 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"); + } + + 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); + + + // 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() + { + 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); + } + } + + 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; + } + + /** 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; + } + + + /** + * 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; + } + + public static void saveProperties() + { + try + { + FileOutputStream out = new FileOutputStream(propertiesFile); + applicationProperties.store(out, "---JalviewX Properties File---"); + out.close(); + } + catch (Exception ex) + { System.out.println("Error saving properties: "+ex); } + } +}