*/
#include "command.hpp"
-#include "coverage.h"
#include "fullmatrix.h"
+#include "libshuff.h"
-using namespace std;
class GlobalData;
class LibShuffCommand : public Command {
- public:
- LibShuffCommand();
- ~LibShuffCommand();
- int execute();
+public:
+ LibShuffCommand(string);
+ LibShuffCommand();
+ ~LibShuffCommand(){};
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ int execute();
+ void help();
+
+private:
+ vector<string> groupNames;
- 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;
-
-
- void setGroups();
- int findIndex(float, int);
- void printCoverageFile(float);
- void printSummaryFile();
-
- GlobalData* globaldata;
- Coverage* coverage;
- FullMatrix* matrix;
- float cutOff;
- int numGroups, numComp, iters;
- string coverageFile, summaryFile;
- ofstream out, outSum;
-
-
+ 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
+ map<string, vector<string> > outputTypes;
};
#endif