public:
ClassifyOtuCommand(string);
- ~ClassifyOtuCommand();
- int execute();
- void help();
+ ClassifyOtuCommand();
+ ~ClassifyOtuCommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "classify.otu"; }
+ string getCommandCategory() { return "Phylotype Analysis"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
private:
ListVector* list;
InputData* input;
- string listfile, namefile, taxfile, label, outputDir;
+ string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
bool abort, allLines, probs;
int cutoff;
set<string> labels; //holds labels to be used
int readTaxonomyFile();
void removeConfidences(string&);
int process(ListVector*);
- string findConcensusTaxonomy(int, ListVector*, int&); // returns the name of the "representative" taxonomy of given bin
+ vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&); // returns the name of the "representative" taxonomy of given bin
};