helpString += "The cluster parameter allows you to indicate whether you want to run the clustering or just split the distance matrix, default=t";
helpString += "The cutoff parameter allow you to set the distance you want to cluster to, default is 0.25. \n";
helpString += "The precision parameter allows you specify the precision of the precision of the distances outputted, default=100, meaning 2 decimal places. \n";
- helpString += "The method allows you to specify what clustering algorythm you want to use, default=average, option furthest, nearest, or average. \n";
+ helpString += "The method allows you to specify what clustering algorithm you want to use, default=average, option furthest, nearest, or average. \n";
helpString += "The splitmethod parameter allows you to specify how you want to split your distance file before you cluster, default=distance, options distance, classify or fasta. \n";
helpString += "The taxonomy parameter allows you to enter the taxonomy file for your sequences, this is only valid if you are using splitmethod=classify. Be sure your taxonomy file does not include the probability scores. \n";
helpString += "The taxlevel parameter allows you to specify the taxonomy level you want to use to split the distance file, default=3, meaning use the first taxon in each list. \n";
m->openOutputFile(listFileName, outList);
outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
-
map<float, int>::iterator itLabel;
+
+ //clears out junk for autocompleting of list files above. Perhaps there is a beter way to handle this from within the data structure?
+ m->printedListHeaders = false;
//for each label needed
for(itLabel = userLabels.begin(); itLabel != userLabels.end(); itLabel++) {
rabund->print(outRabund);
}
//outList << endl;
+ if (!m->printedListHeaders) {
+ m->listBinLabelsInFile.clear(); completeList.printHeaders(outList); }
completeList.print(outList);
if (rabund != NULL) { delete rabund; }
cluster->readPhylipFile(thisDistFile, nameMap);
}else if (countfile != "") {
ct = new CountTable();
- ct->readTable(thisNamefile, false);
+ ct->readTable(thisNamefile, false, false);
cluster->readPhylipFile(thisDistFile, ct);
}
tag = cluster->getTag();
read->read(nameMap);
}else if (countfile != "") {
ct = new CountTable();
- ct->readTable(thisNamefile, false);
+ ct->readTable(thisNamefile, false, false);
read->read(ct);
}else { read->read(nameMap); }