X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=libshuffcommand.h;h=3240860fc329bed3b9551359a6ff1b23a16b8019;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hp=950bb00809a6ba0371906269f9c4804b02c9a0fa;hpb=8770435f2eedcbf4e69daba716144e83da1dd939;p=mothur.git

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 950bb00..3240860 100644
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -11,44 +11,46 @@
  */
 
 #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< vector<float> > > cValues; // vector<vector of coverage scores, one for each comparison.> -one for each distance level.
-		vector< vector<float> > deltaValues; // vector< vector of delta scores, one for each comparison.> -one at each distance
-		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;
-		vector<float> dist;
-		
-		
-		void setGroups();
-		int findIndex(float, int);
-		void printCoverageFile();
-		void printSummaryFile();
-
-		GlobalData* globaldata;
-		Coverage* coverage;
-		FullMatrix* matrix;
-		float cutOff, step;
-		int numGroups, numComp, iters;
-		string coverageFile, summaryFile, form;
-		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