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();
bool abort;
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_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> >&);