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

[mothur.git] / anosimcommand.h

diff --git a/anosimcommand.h b/anosimcommand.h
deleted file mode 100644 (file)
index 4b65070..0000000
--- a/anosimcommand.h
+++ /dev/null
@@ -1,57 +0,0 @@
-#ifndef ANOSIMCOMMAND_H
-#define ANOSIMCOMMAND_H
-
-/*
- *  anosimcommand.h
- *  mothur
- *
- *  Created by westcott on 2/14/11.
- *  Copyright 2011 Schloss Lab. All rights reserved.
- *
- */
-
-
-#include "command.hpp"
-
-class GroupMap;
-
-class AnosimCommand : public Command {
-       
-public:
-       AnosimCommand(string);
-       AnosimCommand();
-       ~AnosimCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "anosim";                                      }
-       string getCommandCategory()             { return "Hypothesis Testing";          }
-       string getHelpString(); 
-       string getCitation() { return "Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\nhttp://www.mothur.org/wiki/Anosim"; }
-       string getDescription()         { return "analysis of similarity"; }
-       
-       int execute();
-       void help() { m->mothurOut(getHelpString()); }
-       
-private:
-       bool abort;
-       GroupMap* designMap;
-       string outputDir, inputDir, designFileName, phylipFileName;
-       
-       vector<vector<double> > convertToRanks(vector<vector<double> >);
-       double calcR(vector<vector<double> >, map<string, vector<int> >);
-       map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
-       double runANOSIM(ofstream&, vector<vector<double> >, map<string, vector<int> >, double);
-       
-       vector< vector<double> > distanceMatrix;
-       vector<string> outputNames;
-       int iters;
-       double experimentwiseAlpha;
-       vector< vector<string> > namesOfGroupCombos;
-       
-       
-};
-
-#endif
-
-
-