// taxa.getTaxon(it).setNameIsDefault(true);
}
// need to make sure newick string consists of indices:
StringBuffer newick = new StringBuffer();
Parser mesqParser = new Parser(pNewick);
String aToken = mesqParser.getNextToken();
int i = 0;
while (!TreebaseUtil.isEmpty(aToken)) {
// logger.debug(" " + i+ ": " + aToken);
String aTokenwithUnderline = StringUtil.blanksToUnderline(aToken);
if (taxonLabelStrToIndexMap.containsKey(aTokenwithUnderline)) {
newick.append(taxonLabelStrToIndexMap.get(aTokenwithUnderline).toString());
} else {
newick.append(aToken);
}
i++;
aToken = mesqParser.getNextToken();
}
if (LOGGER.isDebugEnabled()) {
LOGGER.debug("replace newick=" + newick); //$NON-NLS-1$
}