X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=anosimcommand.h;fp=anosimcommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=4b650705ace41501f3d85d672638a47f48a91ce3;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/anosimcommand.h b/anosimcommand.h
deleted file mode 100644
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
-
-
-