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;
}
