+ void closeLog();
+ string getDefaultPath() { return defaultPath; }
+ void setDefaultPath(string);
+ string getOutputDir() { return outputDir; }
+ void setOutputDir(string);
+
+ string getReleaseDate() { return releaseDate; }
+ void setReleaseDate(string r) { releaseDate = r; }
+ string getVersion() { return version; }
+ void setVersion(string r) { version = r; }
+ vector<string> Groups;
+ vector<string> Treenames;
+ map<string, string> names;
+ vector<string> namesOfGroups;
+ vector<string> binLabelsInFile;
+ vector<string> currentBinLabels;
+ string saveNextLabel, argv, sharedHeaderMode;
+ bool printedHeaders;
+
+ //functions from mothur.h
+ //file operations
+ vector<unsigned long int> divideFile(string, int&);
+ int divideFile(string, int&, vector<string>&);
+ vector<unsigned long int> setFilePosEachLine(string, int&);
+ vector<unsigned long int> setFilePosFasta(string, int&);
+ string sortFile(string, string);
+ void appendFiles(string, string);
+ int renameFile(string, string); //oldname, newname
+ string getFullPathName(string);
+ string hasPath(string);
+ string getExtension(string);
+ string getPathName(string);
+ string getSimpleName(string);
+ string getRootName(string);
+ bool isBlank(string);
+ int openOutputFile(string, ofstream&);
+ int openOutputFileAppend(string, ofstream&);
+ int openInputFile(string, ifstream&);
+ int openInputFile(string, ifstream&, string); //no error given
+ string getline(ifstream&);
+ string getline(istringstream&);
+ void gobble(istream&);
+ void gobble(istringstream&);
+ map<string, int> readNames(string);
+ int readNames(string, map<string, string>&);
+ int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
+ void mothurRemove(string);
+
+ //searchs and checks
+ bool checkReleaseVersion(ifstream&, string);
+ bool anyLabelsToProcess(string, set<string>&, string);
+ bool inUsersGroups(vector<string>, vector<string>);
+ bool inUsersGroups(string, vector<string>);
+ void getNumSeqs(ifstream&, int&);
+ int getNumSeqs(ifstream&);
+ int getNumNames(string);
+ bool isTrue(string);
+ bool isContainingOnlyDigits(string);
+
+
+ //string manipulation
+ void splitAtEquals(string&, string&);
+ void splitAtComma(string&, string&);
+ void splitAtComma(string&, vector<string>&);
+ void splitAtDash(string&, set<int>&);
+ void splitAtDash(string&, set<string>&);
+ void splitAtDash(string&, vector<string>&);
+ void splitAtChar(string&, vector<string>&, char);