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

[mothur.git] / corraxescommand.h

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