*/
#include "command.hpp"
+#include "coverage.h"
+#include "fullmatrix.h"
using namespace std;
int execute();
private:
+ vector< vector< vector<float> > > cValues; // vector<vector of coverage scores, one for each comparison.> -one for each distance level.
+ vector< vector<float> > deltaValues; // vector< vector of delta scores, one for each comparison.> -one at each distance
+ vector<float> sumDelta; //sum of delta scores, one for each comparison.
+ vector<float> sumDeltaSig; //number of random matrixes with that delta value or ??
+ vector< vector<float> > rsumDelta; //vector< vector<sumdelta scores for a given comparison> >
+ vector<string> groupComb;
+ vector<float> dist;
+
+
+ void setGroups();
+ int findIndex(float, int);
+ void printCoverageFile();
+ void printSummaryFile();
+
GlobalData* globaldata;
+ Coverage* coverage;
+ FullMatrix* matrix;
+ float cutOff, step;
+ int numGroups, numComp, iters;
+ string coverageFile, summaryFile, form;
+ ofstream out, outSum;
+
};