X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=homovacommand.h;h=22741e979ec9b0847ca660f5ab41eab49fe715d5;hp=55e4eac7b1a1efc7bac263186fd827bd72d19ad6;hb=615301e57c25e241356a9c2380648d117709458d;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3

diff --git a/homovacommand.h b/homovacommand.h
index 55e4eac..22741e9 100644
--- a/homovacommand.h
+++ b/homovacommand.h
@@ -12,56 +12,43 @@
 
 
 #include "command.hpp"
-#include "inputdata.h"
-#include "sharedrabundvector.h"
-#include "validcalculator.h"
-#include "readphylipvector.h"
 
-class GlobalData;
+//class GlobalData;
+class GroupMap;
 
 class HomovaCommand : public Command {
 	
 public:
 	HomovaCommand(string);
 	HomovaCommand();
-	~HomovaCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	~HomovaCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "homova";					}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "Stewart CN, Excoffier L (1996). Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry). J Evol Biol 9: 153-71. \nhttp://www.mothur.org/wiki/Homova"; }
+	string getDescription()		{ return "homova"; }
+
 	int execute();
-	void help();
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	struct linePair {
-		int start;
-		int num;
-		linePair(int i, int j) : start(i), num(j) {}
-	};
-	vector<linePair> lines;
-	
-	GlobalData* globaldata;
+	double runHOMOVA(ofstream& , map<string, vector<int> >, double);
+	double calcSigleSSWithin(vector<int>);
+	double calcBValue(map<string, vector<int> >, vector<double>&);
+	map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
+
+	bool abort;
+	vector<string> outputNames, Sets;
+
+	string outputDir, inputDir, designFileName, phylipFileName;
 	GroupMap* designMap;
-	map<string, vector<string> > outputTypes;
-	
-	vector< vector<double> > matrix;
-	bool abort, allLines, pickedGroups;
-	set<string> labels; //holds labels to be used
-	string format, groups, label, outputDir, inputDir, designfile, sets, phylipfile, calc, sharedfile;
-	vector<string> Groups, outputNames, Sets;
-	vector< vector<string> > namesOfGroupCombos;
-	int iters, processors;
-	vector<Calculator*> calculators;
-	
-	int driver(int, int, vector<SharedRAbundVector*>, string);
-	int driver(int, int, vector<string>, string, vector< vector<double> >&);
-	int process(vector<SharedRAbundVector*>);
-	int calcHomova(ofstream&, int, vector<string>);
-	map<string, double> calcWithinEach(vector< vector<double> >&, int, vector<string>, map<string, int>&);
-	double calcWithin(vector< vector<double> >&, int, vector<string>);
-	double calcTotal(int);
+	vector< vector<double> > distanceMatrix;
+	int iters;
+	double experimentwiseAlpha;
 };
 
 #endif
-
-