moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / homovacommand.h

diff --git a/homovacommand.h b/homovacommand.h
deleted file mode 100644 (file)
index 4afaeb8..0000000
--- a/homovacommand.h
+++ /dev/null
@@ -1,52 +0,0 @@
-#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