#include "fullmatrix.h"
#include "libshuff.h"
-using namespace std;
class GlobalData;
class LibShuffCommand : public Command {
- public:
- LibShuffCommand();
- ~LibShuffCommand(){};
- int execute();
+public:
+ LibShuffCommand(string);
+ ~LibShuffCommand(){};
+ int execute();
+ void help();
+
+private:
+ vector<string> groupNames;
- private:
- vector<string> groupNames;
-
- 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;
+ void setGroups();
+ int printCoverageFile();
+ int 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, outputDir;
+ vector<string> Groups, outputNames; //holds groups to be used
};
#endif