X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=homovacommand.h;fp=homovacommand.h;h=4afaeb8e3120b42558f5e555c9237474b27a510e;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/homovacommand.h b/homovacommand.h
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+#ifndef HOMOVACOMMAND_H
+#define HOMOVACOMMAND_H
+
+/*
+ *  homovacommand.h
+ *  mothur
+ *
+ *  Created by westcott on 2/8/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+
+//class GlobalData;
+class GroupMap;
+
+class HomovaCommand : public Command {
+	
+public:
+	HomovaCommand(string);
+	HomovaCommand();
+	~HomovaCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "homova";					}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	string getHelpString();	
+	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() { m->mothurOut(getHelpString()); }	
+	
+private:
+	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;
+
+	string outputDir, inputDir, designFileName, phylipFileName;
+	GroupMap* designMap;
+	vector< vector<double> > distanceMatrix;
+	int iters;
+	double experimentwiseAlpha;
+};
+
+#endif