X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=libshuffcommand.h;h=9148576b9135826ffe33b084d833525af182bb5a;hp=fdaa7eee6525ab15ff45407df12544a42e0ae949;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=2d2fbc80f9359b19873ba3e63970b58f4f8f49f3

diff --git a/libshuffcommand.h b/libshuffcommand.h
index fdaa7ee..9148576 100644
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -11,43 +11,50 @@
  */
 
 #include "command.hpp"
-#include "coverage.h"
 #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();	
+    string getOutputPattern(string);	
+	string getCitation() { return "Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001). Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67: 4374-6. \nSchloss PD, Larget BR, Handelsman J (2004). Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol 70: 5485-92. \nhttp://www.mothur.org/wiki/Libshuff"; }
+	string getDescription()		{ return "a generic test that describes whether two or more communities have the same structure using the Cramer-von Mises test statistic"; }
+
+	int execute();
+	void help() { m->mothurOut(getHelpString()); }	
+	
+private:
+	vector<string> groupNames;
+	
+	void setGroups();
+	int printCoverageFile();
+	int printSummaryFile();
 	
-	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();
+	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;
-		Coverage* coverage;
-		FullMatrix* matrix;
-		float cutOff, step;
-		int numGroups, numComp, iters;
-		string coverageFile, summaryFile, form;
-		ofstream out, outSum;
-				
-		
+	bool abort, sim;
+	string outputFile, groups, userform, savegroups, outputDir;
+	vector<string> Groups, outputNames; //holds groups to be used
 };
 
 #endif