~PhylotypeCommand(){}
vector<string> setParameters();
- string getCommandName() { return "phylotype"; }
- string getCommandCategory() { return "OTU-Based Approaches"; }
- string getHelpString();
+ string getCommandName() { return "phylotype"; }
+ string getCommandCategory() { return "Clustering"; }
+ string getHelpString();
+ string getOutputPattern(string);
+ string getCitation() { return "http://www.mothur.org/wiki/Phylotype"; }
+ string getDescription() { return "cluster your sequences into OTUs based on their classifications"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, allLines;
- string taxonomyFileName, label, outputDir, namefile;
+ string taxonomyFileName, label, outputDir, namefile, countfile;
set<string> labels; //holds labels to be used
int cutoff;
map<string, string> namemap;
vector<string> outputNames;
- map<string, vector<string> > outputTypes;
map<int, int> currentNodes;
map<int, int> parentNodes;