+ /**
+ * 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") +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 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); }
+ }
+ /**
+ * 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;
+ Logger lvclient = Logger.getLogger("org.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);
+ }
+