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

[mothur.git] / amovacommand.h

diff --git a/amovacommand.h b/amovacommand.h
deleted file mode 100644 (file)
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
-