class TreeGroupCommand : public Command {
public:
- TreeGroupCommand();
+ TreeGroupCommand(string);
~TreeGroupCommand();
int execute();
+ void help();
private:
void createTree();
InputData* input;
ValidCalculators* validCalculator;
vector<SharedRAbundVector*> lookup;
+ string lastLabel;
string format, outputFile, groupNames, filename;
int numGroups;
ofstream out;
float precision, cutoff;
+ bool abort, allLines;
+ set<int> lines; //hold lines to be used
+ set<string> labels; //holds labels to be used
+ string phylipfile, columnfile, namefile, calc, groups, line, label;
+ vector<string> Estimators, Groups; //holds estimators to be used
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ void process(vector<SharedRAbundVector*>);
+
+
+
};