};
vector<linePair> lines;
- void printSims(ostream&, vector< vector<float> >&);
+ void printSims(ostream&, vector< vector<double> >&);
int process(vector<SharedRAbundVector*>);
vector<Calculator*> matrixCalculators;
InputData* input;
vector<SharedRAbundVector*> lookup;
string exportFileName, output, sharedfile;
- int numGroups, processors;
+ int numGroups, processors, iters, subsampleSize;
ofstream out;
- bool abort, allLines;
+ bool abort, allLines, subsample;
set<string> labels; //holds labels to be used
string outputFile, calc, groups, label, outputDir;
vector<string> Estimators, Groups, outputNames; //holds estimators to be used