public:
SummaryCommand(string);
+ SummaryCommand();
~SummaryCommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
InputData* input;
ValidCalculators* validCalculator;
SAbundVector* sabund;
- string outputFileName;
- ofstream outputFileHandle;
int abund, size;
- bool abort, allLines;
+ bool abort, allLines, groupMode;
set<string> labels; //holds labels to be used
- string label, calc;
+ string label, calc, outputDir;
vector<string> Estimators;
+ vector<string> inputFileNames, outputNames;
+ map<string, vector<string> > outputTypes;
+ vector<string> groups;
+
+ vector<string> parseSharedFile(string);
+ string createGroupSummaryFile(int, int, vector<string>&);
+
};
#endif