X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.h;h=c62b3d668c9a38287769476a598033544d9790a3;hb=37eac2026d91179acda0494c4dcca22f176551b9;hp=22f288a7e768a74c939781df1302e42b92124600;hpb=4956d362c5bc6a47cf7a6290258f0e763e3a406e;p=mothur.git

diff --git a/pcoacommand.h b/pcoacommand.h
index 22f288a..c62b3d6 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.
@@ -11,15 +11,16 @@
  */
  
 #include "command.hpp"
+#include "linearalgebra.h"
 
 
 /*****************************************************************/
-class PCACommand : public Command {
+class PCOACommand : public Command {
 	
 public:
-	PCACommand(string);	
-	PCACommand();
-	~PCACommand();
+	PCOACommand(string);	
+	PCOACommand();
+	~PCOACommand();
 	vector<string> getRequiredParameters();
 	vector<string> getValidParameters();
 	vector<string> getRequiredFiles();
@@ -29,21 +30,18 @@ public:
 	
 private:
 
-	bool abort;
+	bool abort, metric;
 	string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
 	float cutoff, precision;
 	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>);
 	
 };