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();
private:
+ struct linePair {
+ int start;
+ int end;
+ };
+ vector<linePair> lines;
GlobalData* globaldata;
ReadOTUFile* read;
vector<Calculator*> sumCalculators;
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;
+ vector<string> Estimators, Groups, outputNames;
+ map<string, vector<string> > outputTypes;
vector<SharedRAbundVector*> lookup;
- string outputFileName, format, outAllFileName;
- ofstream outputFileHandle, outAll;
- void process(vector<SharedRAbundVector*>);
+ string format, outputDir;
+ int numGroups, processors;
+ int process(vector<SharedRAbundVector*>, string, string);
+ int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
};