//find out the sequences group
string group = groupmap->getGroup(seqName);
+ if (group == "not found") { m->mothurOut(seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); }
+
//do you have a count for this group?
map<string, int>::iterator itGroup = tree[currentNode].groupCount.find(group);
currentNode = childPointer->second;
}else{ //otherwise, error
m->mothurOut("Warning: cannot find taxon " + taxon + " in reference taxonomy tree at level " + toString(tree[currentNode].level) + " for " + seqName + ". This may cause totals of daughter levels not to add up in summary file."); m->mothurOutEndLine();
- seqTaxonomy = "";
+ break;
}
level++;
void PhyloSummary::print(ofstream& out){
try {
//print labels
- out << "taxlevel\t rank ID\t label\t daughterlevels\t total\t";
+ out << "taxlevel\t rankID\t taxon\t daughterlevels\t total\t";
if (groupmap != NULL) {
for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {
out << groupmap->namesOfGroups[i] << '\t';