added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / pcacommand.h

diff --git a/pcacommand.h b/pcacommand.h
index 822be3b905b1a808e74c8b3b59272ca2431cf763..8a36323582b6ca42f153110c48f012148d59cd2b 100644 (file)
--- a/pcacommand.h
+++ b/pcacommand.h
@@ -25,21 +25,18 @@ public:
 private:
 
        bool abort;
-       string phylipfile, columnfile, namefile, format, filename, fbase;
+       string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
        float cutoff, precision;
-       int matrix;
        
        void get_comment(istream&, char, char);
-       void read_mega(istream&, int, vector<string>&, vector<vector<double> >&);
        void read_phylip(istream&, int, vector<string>&, vector<vector<double> >&);
-       void read(string, 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 print_matrix(vector<vector<double> >);
        
 };