-#ifndef PCACOMMAND_H
-#define PCACOMMAND_H
+#ifndef PCOACOMMAND_H
+#define PCOACOMMAND_H
/*
- * pcacommand.h
+ * pcoacommand.h
* Mothur
*
* Created by westcott on 1/4/10.
*/
#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();
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>);
};