X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pcoacommand.h;h=29957f1140e81517cc5a244a696eba7aaf1db49a;hp=22f288a7e768a74c939781df1302e42b92124600;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=4956d362c5bc6a47cf7a6290258f0e763e3a406e

diff --git a/pcoacommand.h b/pcoacommand.h
index 22f288a..29957f1 100644
--- a/pcoacommand.h
+++ b/pcoacommand.h
@@ -1,8 +1,8 @@
-#ifndef PCACOMMAND_H
-#define PCACOMMAND_H
+#ifndef PCOACOMMAND_H
+#define PCOACOMMAND_H
 
 /*
- *  pcacommand.h
+ *  pcoacommand.h
  *  Mothur
  *
  *  Created by westcott on 1/4/10.
@@ -11,39 +11,38 @@
  */
  
 #include "command.hpp"
+#include "linearalgebra.h"
 
 
 /*****************************************************************/
-class PCACommand : public Command {
+class PCOACommand : public Command {
 	
 public:
-	PCACommand(string);	
-	PCACommand();
-	~PCACommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();	
-	void help();
+	PCOACommand(string);	
+	PCOACommand();
+	~PCOACommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "pcoa";					}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	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/Pcoa"; }
+	string getDescription()		{ return "pcoa"; }
+
+	int execute();
+	void help() { m->mothurOut(getHelpString()); }
 	
 private:
 
-	bool abort;
-	string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
-	float cutoff, precision;
+	bool abort, metric;
+	string phylipfile, filename, fbase, outputDir;
 	vector<string> outputNames;
-	map<string, vector<string> > outputTypes;
+	LinearAlgebra linearCalc;
 	
 	void get_comment(istream&, char, char);
-	int read_phylip(istream&, int, vector<string>&, vector<vector<double> >&);
-	void read(string, vector<string>&, vector<vector<double> >&);
-	double pythag(double, double);
-	void matrix_mult(vector<vector<double> >, vector<vector<double> >, vector<vector<double> >&);
-	void recenter(double, vector<vector<double> >, vector<vector<double> >&);
-	void tred2(vector<vector<double> >&, vector<double>&, vector<double>&);
-	void qtli(vector<double>&, vector<double>&, vector<vector<double> >&);
-	void output(string, vector<string>, vector<vector<double> >, vector<double>);
+	void output(string, vector<string>, vector<vector<double> >&, vector<double>);
 	
 };