+private:
+ vector<string> groupNames;
+
+ void setGroups();
+ int printCoverageFile();
+ int printSummaryFile();
+
+ GroupMap* groupMap;
+ FullMatrix* matrix;
+ Libshuff* form;
+ float cutOff, step;
+ int numGroups, numComp, iters;
+ string coverageFile, summaryFile, phylipfile, groupfile;
+ vector<vector<int> > pValueCounts;
+ vector<vector<double> > savedDXYValues;
+ vector<vector<vector<double> > > savedMinValues;
+
+ bool abort, sim;
+ string outputFile, groups, userform, savegroups, outputDir;
+ vector<string> Groups, outputNames; //holds groups to be used