X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=libshuffcommand.h;h=9148576b9135826ffe33b084d833525af182bb5a;hp=3240860fc329bed3b9551359a6ff1b23a16b8019;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 3240860..9148576 100644
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -13,44 +13,48 @@
 #include "command.hpp"
 #include "fullmatrix.h"
 #include "libshuff.h"
+#include "groupmap.h"
 
 
-class GlobalData;
-
 class LibShuffCommand : public Command {
 	
 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();	
+	
+	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();
-
-	GlobalData* globaldata;
+	
+	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, outputNames; //holds groups to be used
-	map<string, vector<string> > outputTypes;
 };
 
 #endif