X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=corraxescommand.h;fp=corraxescommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=2aa7ae0d345cff024b7485ad856013f88895edd9;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/corraxescommand.h b/corraxescommand.h
deleted file mode 100644
index 2aa7ae0..0000000
--- a/corraxescommand.h
+++ /dev/null
@@ -1,57 +0,0 @@
-#ifndef CORRAXESCOMMAND_H
-#define CORRAXESCOMMAND_H
-
-/*
- *  corraxescommand.h
- *  Mothur
- *
- *  Created by westcott on 12/22/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "sharedrabundfloatvector.h"
-#include "inputdata.h"
-
-
-class CorrAxesCommand : public Command {
-public:
-	CorrAxesCommand(string);
-	CorrAxesCommand();
-	~CorrAxesCommand(){}
-	
-	vector<string> setParameters();
-	string getCommandName()			{ return "corr.axes";				}
-	string getCommandCategory()		{ return "Hypothesis Testing";		}
-	string getHelpString();	
-	string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Corr.axes"; }
-	string getDescription()		{ return "calculate the correlation coefficient for each column in a shared/relabund file to the axes displayed in a pcoa file"; }
-	
-	int execute();
-	void help() { m->mothurOut(getHelpString()); }	
-private:
-
-	string axesfile, sharedfile, relabundfile, metadatafile, groups, label, inputFileName, outputDir, method;
-	bool abort, pickedGroups;
-	int numaxes;
-	set<string> names;
-	
-	vector<string> outputNames, Groups;
-	vector<SharedRAbundFloatVector*> lookupFloat;
-	vector<string> metadataLabels;
-	
-	int getSharedFloat(InputData*);
-	int getMetadata();
-	int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);
-	map<string, vector<float> > readAxes();
-	int calcPearson(map<string, vector<float> >&, ofstream&);
-	int calcSpearman(map<string, vector<float> >&, ofstream&);
-	int calcKendall(map<string, vector<float> >&, ofstream&);
-	
-};
-
-
-#endif
-
-