private:
bool abort;
- string phylipfile, columnfile, namefile, format, filename, fbase;
+ string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
float cutoff, precision;
- int matrix;
+ vector<string> outputNames;
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> >&);
+ 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 print_matrix(vector<vector<double> >);
};