public:
ClassifyOtuCommand(string);
+ ClassifyOtuCommand();
~ClassifyOtuCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
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
vector<string> outputNames;
map<string, string> nameMap;
map<string, string> taxMap;
+ map<string, vector<string> > outputTypes;
int readNamesFile();
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
};