#include "command.hpp"
#include "fullmatrix.h"
#include "libshuff.h"
+#include "groupmap.h"
-using namespace std;
-
-class GlobalData;
class LibShuffCommand : public Command {
- public:
- LibShuffCommand();
- ~LibShuffCommand(){};
- int execute();
+public:
+ LibShuffCommand(string);
+ LibShuffCommand();
+ ~LibShuffCommand(){};
+
+ vector<string> setParameters();
+ string getCommandName() { return "libshuff"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+ string getHelpString();
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+private:
+ vector<string> groupNames;
+
+ void setGroups();
+ int printCoverageFile();
+ int printSummaryFile();
- private:
- vector<string> groupNames;
-
- void setGroups();
- void printCoverageFile();
- void 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;
- 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, sim;
+ string outputFile, groups, userform, savegroups, outputDir;
+ vector<string> Groups, outputNames; //holds groups to be used
};
#endif