public static synchronized void createLoggers(boolean reinit) {
if (m_initialized == true && reinit == false) {
return;
}
if (!m_initialized) {
Logger.getLogger("").removeHandler(Logger.getLogger("").getHandlers()[0]);
}
if (m_initialized) {
m_severeLogger.removeHandler(m_severeLogger.getHandlers()[0]);
m_nonSevereLogger.removeHandler(m_nonSevereLogger.getHandlers()[0]);
}
Handler severeHandler = new AMyConsoleHandler(System.err);
severeHandler.setFormatter(new SingleLineFormatter());
m_severeLogger.addHandler(severeHandler);
m_severeLogger.setLevel(getLoggingLevel());
Handler nonSevereHandler = new AMyConsoleHandler(System.out);
nonSevereHandler.setFormatter(new SingleLineFormatter());
m_nonSevereLogger.addHandler(nonSevereHandler);
m_nonSevereLogger.setLevel(getLoggingLevel());
m_initialized = true;
}
public void preprocess(Run run) {
File logFile = new File(getRunDir(run), "genetik.log");
try {
SimpleFileHandler fh = new SimpleFileHandler(logFile);
fh.setFormatter(new CompactFormatter());
Logger logger = Logger.getLogger(GenetikConstants.LOGGER);
logger.setLevel(Level.INFO);
logger.setUseParentHandlers(false);
Handler handlers[] = logger.getHandlers();
logger.addHandler(fh);
for (Handler h : handlers) {
logger.removeHandler(h);
if (h instanceof SimpleFileHandler) h.close(); // close our old one
}
} catch (Exception exp) {
throw new IllegalArgumentException(
"Unable to create log file at " + logFile.getAbsolutePath());
}
super.preprocess(run);
}
public void startFile(String logfile) {
File parent = new File(logfile).getParentFile();
if (!parent.isDirectory() && !parent.mkdirs()) {
logger.warning("Could not create log folder: " + parent);
}
Handler fileHandler = new RotatingFileHandler(logfile);
fileHandler.setFormatter(new DateOutputFormatter(FILE_DATE, false));
logger.addHandler(fileHandler);
}
/** Set up reflection methods required by the loader */
@SuppressWarnings("unchecked")
private boolean prepareLoader() {
try {
// addURL method is used by the class loader to
mAddUrl = URLClassLoader.class.getDeclaredMethod("addURL", URL.class);
mAddUrl.setAccessible(true);
Formatter minecraftLogFormatter = null;
try {
Class<? extends Formatter> formatterClass =
(Class<? extends Formatter>)
Minecraft.class
.getClassLoader()
.loadClass(
ModUtilities.getObfuscatedFieldName(
"net.minecraft.src.ConsoleLogFormatter", "em"));
Constructor<? extends Formatter> defaultConstructor =
formatterClass.getDeclaredConstructor();
defaultConstructor.setAccessible(true);
minecraftLogFormatter = defaultConstructor.newInstance();
} catch (Exception ex) {
ConsoleLogManager.init();
minecraftLogFormatter = ConsoleLogManager.loggerLogManager.getHandlers()[0].getFormatter();
}
logger.setUseParentHandlers(false);
StreamHandler consoleHandler = new ConsoleHandler();
if (minecraftLogFormatter != null) consoleHandler.setFormatter(minecraftLogFormatter);
logger.addHandler(consoleHandler);
FileHandler logFileHandler =
new FileHandler(
new File(Minecraft.getMinecraftDir(), "LiteLoader.txt").getAbsolutePath());
if (minecraftLogFormatter != null) logFileHandler.setFormatter(minecraftLogFormatter);
logger.addHandler(logFileHandler);
} catch (Throwable th) {
logger.log(Level.SEVERE, "Error initialising LiteLoader", th);
return false;
}
return true;
}
private void initLogger() {
ConsoleHandler consoleHandler = null;
Logger rootLogger = LogManager.getLogManager().getLogger("");
Handler[] handlers = rootLogger.getHandlers();
for (Handler handler : handlers) {
if (handler instanceof ConsoleHandler) {
consoleHandler = (ConsoleHandler) handler;
rootLogger.removeHandler(handler);
}
}
logger = Logger.getLogger(contextId);
logger.setLevel(logLevel);
if (!logLevel.equals(Level.OFF)) {
LogFormatter formatter = new LogFormatter();
if (consoleLog) {
if (consoleHandler == null) {
consoleHandler = new ConsoleHandler();
}
consoleHandler.setFormatter(formatter);
consoleHandler.setLevel(logLevel);
logger.addHandler(consoleHandler);
}
String userHomePath = getProperty("user.home", ".");
File logDir = new File(userHomePath, '.' + contextId + "/log");
logDir.mkdirs();
String logFilePattern = new File(logDir, contextId + "-%g.log").getPath();
try {
FileHandler fileHandler = new FileHandler(logFilePattern);
fileHandler.setFormatter(formatter);
fileHandler.setLevel(logLevel);
logger.addHandler(fileHandler);
} catch (IOException e) {
System.err.println("Error: Failed to create log file: " + logFilePattern);
}
}
}
public static Logger initLogger() {
Logger initlogger = Logger.getLogger(settings.getMainClass());
initlogger.setLevel(settings.getLogLevel());
boolean addconsole = false;
if (settings.getLogToFile()) {
try {
Handler handler = new FileHandler(settings.getLogFile(), true);
handler.setFormatter(new SimpleFormatter());
initlogger.addHandler(handler);
} catch (Exception e) {
Logger().warning("Could not set logfile " + settings.getLogFile() + ": " + e.getMessage());
addconsole = true;
}
}
addconsole = settings.getLogToConsole() || addconsole;
if (addconsole) {
initlogger.addHandler(new ConsoleHandler());
}
// restore original log state
logger.setLevel(templevel);
templevel = null;
return initlogger;
}
public UkkonenSuffixTree() {
logger =
Logger.getLogger(
"edu.psu.compbio.seqcode.gse.projects.chipseq.assembler.UkkonenSuffixTree");
isLogging = true;
minLogLevel = Level.SEVERE;
logger.setFilter(new LoggingFilter());
logger.addHandler(new LoggingHandler(System.err, false));
logger.setUseParentHandlers(false);
logger.setLevel(Level.SEVERE);
logger.log(Level.FINE, "Logger setup complete.");
strings = new Vector<TreeString>();
terminal = '$';
root = new TreeNode(null);
totalStringEdges = new Vector<TreeEdge>();
extState = null;
}
public ConsoleManager(GlowServer server) {
this.server = server;
// install Ansi code handler, which makes colors work on Windows
AnsiConsole.systemInstall();
for (Handler h : logger.getHandlers()) {
logger.removeHandler(h);
}
// add log handler which writes to console
logger.addHandler(new FancyConsoleHandler());
// reader must be initialized before standard streams are changed
try {
reader = new ConsoleReader();
} catch (IOException ex) {
logger.log(Level.SEVERE, "Exception initializing console reader", ex);
}
reader.addCompleter(new CommandCompleter());
// set system output streams
System.setOut(new PrintStream(new LoggerOutputStream(Level.INFO), true));
System.setErr(new PrintStream(new LoggerOutputStream(Level.WARNING), true));
// set up colorization replacements
replacements.put(
ChatColor.BLACK,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.BLACK).boldOff().toString());
replacements.put(
ChatColor.DARK_BLUE,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.BLUE).boldOff().toString());
replacements.put(
ChatColor.DARK_GREEN,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.GREEN).boldOff().toString());
replacements.put(
ChatColor.DARK_AQUA,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.CYAN).boldOff().toString());
replacements.put(
ChatColor.DARK_RED,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.RED).boldOff().toString());
replacements.put(
ChatColor.DARK_PURPLE,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.MAGENTA).boldOff().toString());
replacements.put(
ChatColor.GOLD,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.YELLOW).boldOff().toString());
replacements.put(
ChatColor.GRAY,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.WHITE).boldOff().toString());
replacements.put(
ChatColor.DARK_GRAY,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.BLACK).bold().toString());
replacements.put(
ChatColor.BLUE, Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.BLUE).bold().toString());
replacements.put(
ChatColor.GREEN,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.GREEN).bold().toString());
replacements.put(
ChatColor.AQUA, Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.CYAN).bold().toString());
replacements.put(
ChatColor.RED, Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.RED).bold().toString());
replacements.put(
ChatColor.LIGHT_PURPLE,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.MAGENTA).bold().toString());
replacements.put(
ChatColor.YELLOW,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.YELLOW).bold().toString());
replacements.put(
ChatColor.WHITE,
Ansi.ansi().a(Ansi.Attribute.RESET).fg(Ansi.Color.WHITE).bold().toString());
replacements.put(ChatColor.MAGIC, Ansi.ansi().a(Ansi.Attribute.BLINK_SLOW).toString());
replacements.put(ChatColor.BOLD, Ansi.ansi().a(Ansi.Attribute.UNDERLINE_DOUBLE).toString());
replacements.put(
ChatColor.STRIKETHROUGH, Ansi.ansi().a(Ansi.Attribute.STRIKETHROUGH_ON).toString());
replacements.put(ChatColor.UNDERLINE, Ansi.ansi().a(Ansi.Attribute.UNDERLINE).toString());
replacements.put(ChatColor.ITALIC, Ansi.ansi().a(Ansi.Attribute.ITALIC).toString());
replacements.put(ChatColor.RESET, Ansi.ansi().a(Ansi.Attribute.RESET).toString());
}
public void addHandler(Handler h) {
initializeGlobalHandlers();
super.addHandler(h);
}
