+ void setGroups();
+ void printCoverageFile();
+ void printSummaryFile();
+
+ GlobalData* globaldata;
+ FullMatrix* matrix;
+ Libshuff* form;
+ float cutOff, step;
+ int numGroups, numComp, iters;
+ string coverageFile, summaryFile;
+ vector<vector<int> > pValueCounts;
+ vector<vector<double> > savedDXYValues;
+ vector<vector<vector<double> > > savedMinValues;
+
+ bool abort;
+ string outputFile, groups, userform, savegroups;
+ vector<string> Groups; //holds groups to be used