vector<string> setParameters();
string getCommandName() { return "cluster.classic"; }
string getCommandCategory() { return "Clustering"; }
+
string getHelpString();
- string getCitation() { return "http://www.mothur.org/wiki/Cluster.classic"; }
+ string getOutputPattern(string);
+ string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219.\nSchloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6.\nhttp://www.mothur.org/wiki/Cluster.classic\n";}
+ string getDescription() { return "cluster your sequences into OTUs using DOTUR’s method"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, hard, sim;
- string method, fileroot, tag, outputDir, phylipfile, namefile;
+ string method, fileroot, tag, outputDir, phylipfile, namefile, countfile;
double cutoff;
int precision, length;
ofstream sabundFile, rabundFile, listFile;