X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=amovacommand.h;fp=amovacommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=50dc81a517dbbe89f39d9a4e1ca858ed3488a402;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/amovacommand.h b/amovacommand.h
deleted file mode 100644
index 50dc81a..0000000
--- a/amovacommand.h
+++ /dev/null
@@ -1,50 +0,0 @@
-#ifndef AMOVACOMMAND_H
-#define AMOVACOMMAND_H
-
-/*
- *  amovacommand.h
- *  mothur
- *
- *  Created by westcott on 2/7/11.
- *  Copyright 2011 Schloss Lab. All rights reserved.
- *
- */
-
-#include "command.hpp"
-class GroupMap;
-
-class AmovaCommand : public Command {
-	
-public:
-	AmovaCommand(string);
-	AmovaCommand();
-	~AmovaCommand() {}
-	
-	vector<string> setParameters();
-	string getCommandName()			{ return "amova";					}
-	string getCommandCategory()		{ return "Hypothesis Testing";		}
-	string getHelpString();	
-	string getCitation() { return "Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\nhttp://www.mothur.org/wiki/Amova"; }
-	string getDescription()		{ return "analysis of molecular variance"; }
-	
-	int execute();
-	void help() { m->mothurOut(getHelpString()); }
-	
-private:
-	double runAMOVA(ofstream&, map<string, vector<int> >, double);
-	double calcSSWithin(map<string, vector<int> >&);
-	double calcSSTotal(map<string, vector<int> >&);
-	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
-