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
+ int openInputFile(string, ifstream&, string); //no error given
+
+ bool checkLocations(string&, string); //filename, inputDir. checks for file in ./, inputdir, default and mothur's exe location. Returns false if cant be found. If found completes name with location
string getline(ifstream&);
string getline(istringstream&);
void gobble(istream&);
bool isTrue(string);
bool isContainingOnlyDigits(string);
bool isNumeric1(string);
+ bool isLabelEquivalent(string, string);
+ string getSimpleLabel(string);
+ string findEdianness();
//string manipulation
string makeList(vector<string>&);
bool isSubset(vector<string>, vector<string>); //bigSet, subset
int checkName(string&);
+ map<string, vector<string> > parseClasses(string);
//math operation
+ double max(vector<double>&); //returns largest value in vector
+ double min(vector<double>&); //returns smallest value in vector
int factorial(int num);
vector<vector<double> > binomial(int);
float ceilDist(float, int);
float roundDist(float, int);
unsigned int fromBase36(string);
+ double median(vector<double>);
int getRandomIndex(int); //highest
double getStandardDeviation(vector<int>&);
vector<double> getStandardDeviation(vector< vector<double> >&);