/* * 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.*; import org.biojava.dasobert.dasregistry.Das1Source; /** * 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"; public static final String DAS_REGISTRY_URL = "DAS_REGISTRY_URL"; public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_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); } /** * generate Das1Sources from the local das source list * @return Vector of Das1Sources */ public static Vector getLocalDasSources() { Vector localSources = new Vector(); String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE"); if (local != null) { StringTokenizer st = new StringTokenizer(local, "\t"); while (st.hasMoreTokens()) { String token = st.nextToken(); int bar = token.indexOf("|"); Das1Source source = new Das1Source(); source.setUrl(token.substring(bar + 1)); if (source.getUrl().startsWith("sequence:")) { source.setUrl(source.getUrl().substring(9)); // this source also serves sequences as well as features source.setCapabilities(new String[] { "sequence", "features"}); } else { // default is that all user added sources serve features source.setCapabilities(new String[] { "features"}); } source.setNickname(token.substring(0, bar)); localSources.addElement(source); } } return localSources; } }