class TreeGroupCommand : public Command {
public:
- TreeGroupCommand();
+ TreeGroupCommand(string);
+ TreeGroupCommand();
~TreeGroupCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
+ void help();
private:
- void createTree();
+ int createTree();
void printSims(ostream&);
- void makeSimsShared();
- void makeSimsDist();
+ int makeSimsShared();
+ int makeSimsDist();
GlobalData* globaldata;
ReadOTUFile* read;
InputData* input;
ValidCalculators* validCalculator;
vector<SharedRAbundVector*> lookup;
+ string lastLabel;
string format, outputFile, groupNames, filename;
int numGroups;
ofstream out;
float precision, cutoff;
+ map<string, vector<string> > outputTypes;
+
+ bool abort, allLines;
+ set<string> labels; //holds labels to be used
+ string phylipfile, columnfile, namefile, calc, groups, label, outputDir;
+ vector<string> Estimators, Groups, outputNames; //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.
+ int process(vector<SharedRAbundVector*>);
+
+
};