/*
* pcacommand.h
- * Mothur
+ * mothur
*
- * Created by westcott on 1/4/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
+ * Created by westcott on 1/7/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
*
*/
-
-#include "command.hpp"
+#include "command.hpp"
+#include "linearalgebra.h"
+#include "sharedrabundfloatvector.h"
/*****************************************************************/
class PCACommand : public Command {
public:
PCACommand(string);
- ~PCACommand();
- int execute();
- void help();
+ PCACommand();
+ ~PCACommand() {}
+
+ vector<string> setParameters();
+ string getCommandName() { return "pca"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+ 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/Pca"; }
+ string getDescription() { return "pca"; }
+
+ 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 outputDir, mode, inputFile, label, groups, sharedfile, relabundfile;
+ vector<string> outputNames, Groups;
+ set<string> labels;
+ LinearAlgebra linearCalc;
- void get_comment(istream&, char, char);
- void 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> > createMatrix(vector<SharedRAbundFloatVector*>);
+ int process(vector<SharedRAbundFloatVector*>&);
+ void output(string, vector<string>, vector<vector<double> >&, vector<double>);
};
-
+
/*****************************************************************/
-
+
#endif
+