X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=libshuffcommand.h;h=1e5726dd770f928b62ca8ef07fa3c24150c0a8b5;hb=cd37904452dc95b183ff313ff05720c562902487;hp=fdaa7eee6525ab15ff45407df12544a42e0ae949;hpb=2d2fbc80f9359b19873ba3e63970b58f4f8f49f3;p=mothur.git

diff --git a/libshuffcommand.h b/libshuffcommand.h
index fdaa7ee..1e5726d 100644
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -11,43 +11,40 @@
  */
 
 #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(){};
+	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, step;
-		int numGroups, numComp, iters;
-		string coverageFile, summaryFile, form;
-		ofstream out, outSum;
-				
-		
+	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;
+
+	bool abort;
+	string outputFile, groups, userform, savegroups;
+	vector<string> Groups; //holds groups to be used
 };
 
 #endif