vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
vector<string> Treenames;
- //map<string, string> names;
- vector<string> binLabelsInFile;
- vector<string> currentBinLabels;
+ vector<string> sharedBinLabelsInFile;
+ vector<string> currentSharedBinLabels;
+ vector<string> listBinLabelsInFile;
string saveNextLabel, argv, sharedHeaderMode, groupMode;
- bool printedHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
+ bool printedSharedHeaders, printedListHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
//functions from mothur.h
//file operations
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&);
bool isTrue(string);
bool isContainingOnlyDigits(string);
bool isNumeric1(string);
+ bool isLabelEquivalent(string, string);
+ string getSimpleLabel(string);
+ string findEdianness();
//string manipulation
map<string, vector<string> > parseClasses(string);
//math operation
+ double max(vector<double>&); //returns largest value in vector
+ double min(vector<double>&); //returns smallest value in vector
int factorial(int num);
vector<vector<double> > binomial(int);
float ceilDist(float, int);
float roundDist(float, int);
unsigned int fromBase36(string);
+ double median(vector<double>);
int getRandomIndex(int); //highest
double getStandardDeviation(vector<int>&);
vector<double> getStandardDeviation(vector< vector<double> >&);
counttablefile = "";
summaryfile = "";
gui = false;
- printedHeaders = false;
+ printedSharedHeaders = false;
+ printedListHeaders = false;
commandInputsConvertError = false;
mothurCalling = false;
debug = false;