maxLevel = 0;
calcTotals = true;
string name, tax;
- addSeqToTree("unknown", "unknown;");
-
#ifdef USE_MPI
int pid, num, processors;
#endif
assignHeirarchyIDs(0);
-
+
+
+ string unknownTax = "unknown;";
+ //added last taxon until you get desired level
+ for (int i = 1; i < maxLevel; i++) {
+ unknownTax += "unclassfied;";
+ }
+
+ addSeqToTree("unknown", unknownTax);
+
//create file for summary if needed
setUp(tfile);
}
map<string, int>::iterator itFind;
map<string, int> taxonomyFileNames = name2Taxonomy;
+ if (m->debug) { m->mothurOut("[DEBUG]: in error check. Numseqs in template = " + toString(templateFileNames.size()) + ". Numseqs in taxonomy = " + toString(taxonomyFileNames.size()) + ".\n"); }
+
for (int i = 0; i < templateFileNames.size(); i++) {
itFind = taxonomyFileNames.find(templateFileNames[i]);
if (itFind != taxonomyFileNames.end()) { //found it so erase it
taxonomyFileNames.erase(itFind);
}else {
- m->mothurOut(templateFileNames[i] + " is in your template file and is not in your taxonomy file. Please correct."); m->mothurOutEndLine();
+ m->mothurOut("'" +templateFileNames[i] + "' is in your template file and is not in your taxonomy file. Please correct."); m->mothurOutEndLine();
okay = false;
}