public:
PCACommand(string);
+ PCACommand();
~PCACommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
bool abort;
- string phylipfile, columnfile, namefile, format, filename, fbase;
+ string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
float cutoff, precision;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
void get_comment(istream&, char, char);
- void read_mega(istream&, vector<string>&, vector<vector<double> >&);
- void read_phylip(istream&, 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 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> >);
};