X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=libshuffcommand.h;h=81ae17ab644287e75a2de30f88427a67937b549d;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=da5f9e8c1d3d06cd7ad3812578ec83bf6bff5774;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/libshuffcommand.h b/libshuffcommand.h
index da5f9e8..81ae17a 100644
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -13,38 +13,47 @@
 #include "command.hpp"
 #include "fullmatrix.h"
 #include "libshuff.h"
+#include "groupmap.h"
 
 
-class GlobalData;
-
 class LibShuffCommand : public Command {
 	
 public:
-	LibShuffCommand(string);	
+	LibShuffCommand(string);
+	LibShuffCommand();	
 	~LibShuffCommand(){};
-	int execute();
-	void help();	
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "libshuff";				}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	string getOutputFileNameTag(string, string);
+	string getHelpString();	
+	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();
-	void printCoverageFile();
-	void printSummaryFile();
-
-	GlobalData* globaldata;
+	int printCoverageFile();
+	int printSummaryFile();
+	
+	GroupMap* groupMap;
 	FullMatrix* matrix;
 	Libshuff* form;
 	float cutOff, step;
 	int numGroups, numComp, iters;
-	string coverageFile, summaryFile;
+	string coverageFile, summaryFile, phylipfile, groupfile;
 	vector<vector<int> > pValueCounts;
 	vector<vector<double> > savedDXYValues;
 	vector<vector<vector<double> > > savedMinValues;
 
-	bool abort;
+	bool abort, sim;
 	string outputFile, groups, userform, savegroups, outputDir;
-	vector<string> Groups; //holds groups to be used
+	vector<string> Groups, outputNames; //holds groups to be used
 };
 
 #endif