public void importData() throws IOException, DaoException {
MySQLbulkLoader.bulkLoadOn();
FileReader reader = new FileReader(geneFile);
BufferedReader buf = new BufferedReader(reader);
String line = buf.readLine();
DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance();
while (line != null) {
if (pMonitor != null) {
pMonitor.incrementCurValue();
ConsoleUtil.showProgress(pMonitor);
}
if (!line.startsWith("#")) {
String parts[] = line.split("\t");
int entrezGeneId = Integer.parseInt(parts[1]);
String geneSymbol = parts[2];
Set<String> aliases;
if (parts[4].equals("-")) {
aliases = Collections.emptySet();
} else {
aliases = new HashSet<String>(Arrays.asList(parts[4].split("\\|")));
}
CanonicalGene gene = new CanonicalGene(entrezGeneId, geneSymbol, aliases);
daoGene.addGene(gene);
}
line = buf.readLine();
}
if (MySQLbulkLoader.isBulkLoad()) {
daoGene.flushGenesToDatabase();
}
}
