X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.h;h=93feefa3dec06bc6084055fc701a6cd8baf058de;hb=44f3a3c81a34fdee62550d98838a4b421e8df08e;hp=ea1738b9113f967af45f52e0978f4d48dcd1b23f;hpb=1b4b18b3e6fa1436b7cc6dcb14c749ac1ae1bdd8;p=mothur.git

diff --git a/pcoacommand.h b/pcoacommand.h
index ea1738b..93feefa 100644
--- a/pcoacommand.h
+++ b/pcoacommand.h
@@ -11,6 +11,7 @@
  */
  
 #include "command.hpp"
+#include "linearalgebra.h"
 
 
 /*****************************************************************/
@@ -19,33 +20,28 @@ class PCOACommand : public Command {
 public:
 	PCOACommand(string);	
 	PCOACommand();
-	~PCOACommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();	
-	void help();
+	~PCOACommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "pcoa";					}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	string getOutputFileNameTag(string, string);
+	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/Pcoa"; }
+	string getDescription()		{ return "pcoa"; }
+
+	int execute();
+	void help() { m->mothurOut(getHelpString()); }
 	
 private:
 
 	bool abort, metric;
-	string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
-	float cutoff, precision;
+	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>);
-	vector< vector<double> > calculateEuclidianDistance(vector<vector<double> >&, int);
-	double calcPearson(vector<vector<double> >&, vector<vector<double> >&);
 	
 };