public:
GetRelAbundCommand(string);
+ GetRelAbundCommand();
~GetRelAbundCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
InputData* input;
vector<SharedRAbundVector*> lookup;
- bool abort, allLines;
+ bool abort, allLines, pickedGroups;
set<string> labels; //holds labels to be used
string groups, label, outputDir, scale;
- vector<string> Groups;
+ vector<string> Groups, outputNames;
+ map<string, vector<string> > outputTypes;
- int getRelAbundance(vector<SharedRAbundVector*>, ofstream&);
+ int getRelAbundance(vector<SharedRAbundVector*>&, ofstream&);
};