finished chimera.slayer adding trim parameter, added persample parameter to sub.sampl...

[mothur.git] / pcoacommand.h

diff --git a/pcoacommand.h b/pcoacommand.h
index ea1738b9113f967af45f52e0978f4d48dcd1b23f..8bb7c1bdc586798b70fb3ec3f601bf13b5a16d9e 100644 (file)
--- a/pcoacommand.h
+++ b/pcoacommand.h
@@ -11,6 +11,7 @@
  */
  
 #include "command.hpp"
+#include "linearalgebra.h"
 
 
 /*****************************************************************/
@@ -34,15 +35,12 @@ private:
        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>);
        vector< vector<double> > calculateEuclidianDistance(vector<vector<double> >&, int);
        double calcPearson(vector<vector<double> >&, vector<vector<double> >&);