public:
SummarySharedCommand(string);
+ SummarySharedCommand();
~SummarySharedCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
InputData* input;
ValidCalculators* validCalculator;
- bool abort, allLines, mult, all;
+ bool abort, allLines, mult, all, createPhylip;
set<string> labels; //holds labels to be used
string label, calc, groups;
vector<string> Estimators, Groups, outputNames;
+ map<string, vector<string> > outputTypes;
vector<SharedRAbundVector*> lookup;
string format, outputDir;
int numGroups, processors;
int process(vector<SharedRAbundVector*>, string, string);
- int driver(vector<SharedRAbundVector*>, int, int, string, string);
+ int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
};