vector<string> binLabelsInFile;
vector<string> currentBinLabels;
string saveNextLabel, argv, sharedHeaderMode;
- bool printedHeaders;
+ bool printedHeaders, commandInputsConvertError;
//functions from mothur.h
//file operations
vector<unsigned long long> setFilePosEachLine(string, int&);
vector<unsigned long long> setFilePosFasta(string, int&);
string sortFile(string, string);
- void appendFiles(string, string);
+ int appendFiles(string, string);
int renameFile(string, string); //oldname, newname
string getFullPathName(string);
string hasPath(string);
void gobble(istringstream&);
map<string, int> readNames(string);
int readNames(string, map<string, string>&);
+ int readNames(string, map<string, vector<string> >&);
int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
- void mothurRemove(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, 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.
+
//searchs and checks
bool checkReleaseVersion(ifstream&, string);
void getNumSeqs(ifstream&, int&);
int getNumSeqs(ifstream&);
int getNumNames(string);
+ int getNumChar(string, char);
bool isTrue(string);
bool isContainingOnlyDigits(string);
+ bool isNumeric1(string);
//string manipulation
void splitAtDash(string&, set<string>&);
void splitAtDash(string&, vector<string>&);
void splitAtChar(string&, vector<string>&, char);
+ int removeConfidences(string&);
//math operation
int factorial(int num);
flowfile = "";
gui = false;
printedHeaders = false;
+ commandInputsConvertError = false;
sharedHeaderMode = "";
}
~MothurOut();