*/
#include "command.hpp"
-#include "coverage.h"
#include "fullmatrix.h"
+#include "libshuff.h"
-using namespace std;
class GlobalData;
public:
LibShuffCommand();
- ~LibShuffCommand();
+ ~LibShuffCommand(){};
int execute();
private:
- vector< vector<float> > cValues; // vector of coverage scores, one for each comparison.
- vector<float> deltaValues; // vector of delta scores, one for each comparison.
- 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<string> groupNames;
void setGroups();
- int findIndex(float, int);
- void printCoverageFile(float);
+ void printCoverageFile();
void printSummaryFile();
GlobalData* globaldata;
- Coverage* coverage;
FullMatrix* matrix;
- float cutOff;
+ Libshuff* form;
+ float cutOff, step;
int numGroups, numComp, iters;
string coverageFile, summaryFile;
- ofstream out, outSum;
-
-
+ vector<vector<int> > pValueCounts;
+ vector<vector<double> > savedDXYValues;
+ vector<vector<vector<double> > > savedMinValues;
};
#endif