int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
int mothurRemove(string);
bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
+ bool mothurConvert(string, intDist&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
bool mothurConvert(string, float&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
bool mothurConvert(string, double&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
void splitAtChar(string&, vector<string>&, char);
void splitAtChar(string&, string&, char);
int removeConfidences(string&);
+ string removeQuotes(string);
string makeList(vector<string>&);
+ bool isSubset(vector<string>, vector<string>); //bigSet, subset
//math operation
int factorial(int num);
float roundDist(float, int);
unsigned int fromBase36(string);
int getRandomIndex(int); //highest
+ double getStandardDeviation(vector<int>&);
int control_pressed;
bool executing, runParse, jumble, gui, mothurCalling, debug;