string getRootName(string);
bool isBlank(string);
int openOutputFile(string, ofstream&);
+ int openOutputFileBinary(string, ofstream&);
int openOutputFileAppend(string, ofstream&);
+ int openOutputFileBinaryAppend(string, ofstream&);
int openInputFile(string, ifstream&);
int openInputFile(string, ifstream&, string); //no error given
string getline(ifstream&);
map<string, int> readNames(string);
map<string, int> readNames(string, unsigned long int&);
int readTax(string, map<string, string>&);
+ vector<consTax> readConsTax(string);
+ int readConsTax(string, map<string, consTax2>&);
int readNames(string, map<string, string>&, map<string, int>&);
int readNames(string, map<string, string>&);
int readNames(string, map<string, string>&, bool);
string makeList(vector<string>&);
bool isSubset(vector<string>, vector<string>); //bigSet, subset
int checkName(string&);
+ map<string, vector<string> > parseClasses(string);
//math operation
int factorial(int num);
vector<double> getStandardDeviation(vector< vector<double> >&);
vector<double> getStandardDeviation(vector< vector<double> >&, vector<double>&);
vector<double> getAverages(vector< vector<double> >&);
+ double getAverage(vector<double>);
vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&);
vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&, vector< vector<seqDist> >&);
vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&, string);