void mothurOutEndLine(); //writes to cout and the logfile
void mothurOut(string, ofstream&); //writes to the ofstream, cout and the logfile
void mothurOutEndLine(ofstream&); //writes to the ofstream, cout and the logfile
+ void mothurOutJustToScreen(string); //writes to cout
void mothurOutJustToLog(string);
void errorOut(exception&, string, string);
void closeLog();
vector<string> binLabelsInFile;
vector<string> currentBinLabels;
string saveNextLabel, argv, sharedHeaderMode, groupMode;
- bool printedHeaders, commandInputsConvertError, changedSeqNames;
+ bool printedHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
//functions from mothur.h
//file operations
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);
sharedHeaderMode = "";
groupMode = "group";
changedSeqNames = false;
+ modifyNames = true;
}
~MothurOut();