*/
#include "command.hpp"
+#include "linearalgebra.h"
/*****************************************************************/
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 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, 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> >&);
};