vector<string> binLabelsInFile;
vector<string> currentBinLabels;
string saveNextLabel, argv, sharedHeaderMode, groupMode;
- bool printedHeaders, commandInputsConvertError;
+ bool printedHeaders, commandInputsConvertError, changedSeqNames;
//functions from mothur.h
//file operations
set<string> readAccnos(string);
int readAccnos(string, vector<string>&);
map<string, int> readNames(string);
+ map<string, int> readNames(string, unsigned long int&);
int readTax(string, map<string, string>&);
int readNames(string, map<string, string>&, map<string, int>&);
int readNames(string, map<string, string>&);
string removeQuotes(string);
string makeList(vector<string>&);
bool isSubset(vector<string>, vector<string>); //bigSet, subset
+ int checkName(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> >&);
+ 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);
+ vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&);
int control_pressed;
bool executing, runParse, jumble, gui, mothurCalling, debug;
debug = false;
sharedHeaderMode = "";
groupMode = "group";
+ changedSeqNames = false;
}
~MothurOut();