if(it != container.end()){ //no parameter given
if(isFile == true) {
+
+ int pos = (it->second).find(".tx.");
+ if (pos != string::npos) { m->sharedHeaderMode = "tax"; }
+ else { m->sharedHeaderMode = "otu"; }
#ifdef USE_MPI
int pid, processors;
m->mothurOut("Unable to open " + container[parameter]); m->mothurOutEndLine();
return "not open";
}
+
+ //check phylip file to make sure its really phylip and not column
+ if ((it->first == "phylip") && (ableToOpen != 1)) {
+ ifstream inPhylip;
+ m->openInputFile(it->second, inPhylip);
+
+ string numTest, name;
+ inPhylip >> numTest >> name;
+ inPhylip.close();
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ". I suspect you entered a column formatted file as a phylip file, aborting."); m->mothurOutEndLine(); return "not found"; }
+ }
}
}else { return "not found"; }