vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
vector<string> Treenames;
- //map<string, string> names;
vector<string> sharedBinLabelsInFile;
vector<string> currentSharedBinLabels;
vector<string> listBinLabelsInFile;
- //vector<string> currentListBinLabels;
string saveNextLabel, argv, sharedHeaderMode, groupMode;
bool printedSharedHeaders, printedListHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
vector<unsigned long long> setFilePosFasta(string, int&);
string sortFile(string, string);
int appendFiles(string, string);
+ int appendBinaryFiles(string, string);
int appendFilesWithoutHeaders(string, string);
int renameFile(string, string); //oldname, newname
string getFullPathName(string);
int openOutputFileAppend(string, ofstream&);
int openOutputFileBinaryAppend(string, ofstream&);
int openInputFile(string, ifstream&);
- int openInputFile(string, ifstream&, string); //no error given
+ int openInputFileBinary(string, ifstream&);
+ int openInputFileBinary(string, ifstream&, string);
+ 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&);