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);
}
/** 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;
}
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;
}
