public:
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;
- vector<SharedRAbundVector*> lastLookup;
+ string lastLabel;
string format, outputFile, groupNames, filename;
int numGroups;
ofstream out;
float precision, cutoff;
+ map<string, vector<string> > outputTypes;
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
+ 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.
- void process(vector<SharedRAbundVector*>);
+ int process(vector<SharedRAbundVector*>);