X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=libshuffcommand.h;h=da5f9e8c1d3d06cd7ad3812578ec83bf6bff5774;hb=c3f0a9c8f932b923f3a6fbbf143e8f4b85fd6f5f;hp=18bfadef5497316b27721a4d740c526cc3eec83a;hpb=197c6d3303439582502840980d6a85cf3aab2314;p=mothur.git

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 18bfade..da5f9e8 100644
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -14,33 +14,37 @@
 #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();
+	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, outputDir;
+	vector<string> Groups; //holds groups to be used
 };
 
 #endif