X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCache.java;h=e5f7f7b850673ca6fe2206f6f337b4d129db7ddb;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=e2477d9eab317abb2452fff15073bfd7a4f3770f;hpb=086115440f8e30fa1bfc881e00b94878b491fb89;p=jalview.git diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index e2477d9..e5f7f7b 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1,174 +1,486 @@ -/* - * 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 java.net.*; - - -/** - * 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) - *
jalview.browser - used in the jalview.utils.browserLauncher class if it doesn't know what else to do. - *
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 -{ - - /** Jalview Properties */ - public static Properties applicationProperties; - - /** Default file is ~/.jalview_properties */ - static String propertiesFile; - - /** Called when Jalview is started */ - public static void loadProperties(String propsFile) - { - applicationProperties = new Properties(); - 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); - } - - // 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"; - } - - // jnlpVersion will be null if we're using InstallAnywhere - if(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) - { jnlpVersion = codeVersion; } - } - - System.out.println("Version: "+codeVersion); - System.out.println("Latest : "+jnlpVersion); - - setProperty("LATEST_VERSION", jnlpVersion); - 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 applicationProperties.getProperty(key); - } - - /** - * 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) - { - } - - return obj; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) + * Copyright (C) 2008 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.*; + +/** + * 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 $Revision$ + */ +public class Cache +{ + /** + * property giving log4j level for CASTOR loggers + */ + public static final String CASTORLOGLEVEL = "logs.Castor.level"; + + /** + * property giving log4j level for AXIS loggers + */ + public static final String AXISLOGLEVEL = "logs.Axis.level"; + + /** + * property giving log4j level for Jalview Log + */ + public static final String JALVIEWLOGLEVEL = "logs.Jalview.level"; + + public static final String DAS_LOCAL_SOURCE = "DAS_LOCAL_SOURCE"; + + /** + * Initialises the Jalview Application Log + */ + 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 + { + ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(), + "System.err"); + ap.setName("JalviewLogger"); + org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for + // log output + Logger laxis = Logger.getLogger("org.apache.axis"); + Logger lcastor = Logger.getLogger("org.exolab.castor"); + jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview"); + + laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level", + Level.INFO.toString()))); + lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", + Level.INFO.toString()))); + lcastor = Logger.getLogger("org.exolab.castor.xml"); + lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", + Level.INFO.toString()))); + // lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller"); + // lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level", + // Level.INFO.toString()))); + jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault( + "logs.Jalview.level", Level.INFO.toString()))); + // laxis.addAppender(ap); + // lcastor.addAppender(ap); + // jalview.bin.Cache.log.addAppender(ap); + // Tell the user that debug is enabled + jalview.bin.Cache.log.debug("Jalview Debugging Output Follows."); + } catch (Exception ex) + { + System.err.println("Problems initializing the log4j system\n"); + ex.printStackTrace(System.err); + } + } + + /** Called when Jalview is started */ + public static void loadProperties(String propsFile) + { + propertiesFile = propsFile; + if (propsFile == null) + { + propertiesFile = System.getProperty("user.home") + File.separatorChar + + ".jalview_properties"; + } + + 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 orgtimeout = System + .getProperty("sun.net.client.defaultConnectTimeout"); + if (orgtimeout == null) + { + orgtimeout = "30"; + System.out.println("# INFO: Setting default net timeout to " + + orgtimeout + " seconds."); + } + String jnlpVersion = null; + try + { + System.setProperty("sun.net.client.defaultConnectTimeout", + "5000"); + 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("Non-fatal exceptions when checking version at www.jalview.org :"); + System.out.println(ex); + jnlpVersion = getProperty("VERSION"); + } + System.setProperty("sun.net.client.defaultConnectTimeout", + orgtimeout); + + 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); + } + } + + /** + * 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."); + } + } 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."); + } + } catch (Exception e) + { + groovyJarsArePresent = 0; + jalview.bin.Cache.log.debug("Groovy Classes are not present"); + } + } + return (groovyJarsArePresent > 0); + } + +}