static MothurOut* getInstance();
void setFileName(string);
- void mothurOut(string);
- void mothurOutEndLine();
+ void mothurOut(string); //writes to cout and the logfile
+ void mothurOutEndLine(); //writes to cout and the logfile
+ void mothurOut(string, ofstream&); //writes to the ofstream, cout and the logfile
+ void mothurOutEndLine(ofstream&); //writes to the ofstream, cout and the logfile
void mothurOutJustToLog(string);
void errorOut(exception&, string, string);
void closeLog();
vector<string> Treenames;
map<string, string> names;
vector<string> namesOfGroups;
- string saveNextLabel, argv;
+ 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 gobble(istream&);
void gobble(istringstream&);
map<string, int> readNames(string);
+ int readNames(string, map<string, string>&);
+ int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
//searchs and checks
bool checkReleaseVersion(ifstream&, string);
int getNumSeqs(ifstream&);
int getNumNames(string);
bool isTrue(string);
+ bool isContainingOnlyDigits(string);
//string manipulation
float ceilDist(float, int);
float roundDist(float, int);
unsigned int fromBase36(string);
+ int getRandomIndex(int); //highest
int control_pressed;
- bool executing, runParse, jumble;
+ bool executing, runParse, jumble, gui;
//current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
string getPhylipFile() { return phylipfile; }
string getOligosFile() { return oligosfile; }
string getAccnosFile() { return accnosfile; }
string getTaxonomyFile() { return taxonomyfile; }
+ string getFlowFile() { return flowfile; }
string getProcessors() { return processors; }
void setListFile(string f) { listfile = getFullPathName(f); }
void setOligosFile(string f) { oligosfile = getFullPathName(f); }
void setAccnosFile(string f) { accnosfile = getFullPathName(f); }
void setTaxonomyFile(string f) { taxonomyfile = getFullPathName(f); }
+ void setFlowFile(string f) { flowfile = getFullPathName(f); }
void setProcessors(string p) { processors = p; }
void printCurrentFiles();
+ bool hasCurrentFiles();
void clearCurrentFiles();
private:
accnosfile = "";
taxonomyfile = "";
processors = "1";
+ flowfile = "";
+ gui = false;
+ printedHeaders = false;
+ sharedHeaderMode = "";
};
~MothurOut();
string releaseDate, version;
string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
- string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors;
+ string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
ofstream out;