vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
vector<string> Treenames;
- map<string, string> names;
+ //map<string, string> names;
vector<string> binLabelsInFile;
vector<string> currentBinLabels;
string saveNextLabel, argv, sharedHeaderMode;
//functions from mothur.h
//file operations
+ bool dirCheck(string&); //completes path, appends appropriate / or \, makes sure dir is writable.
vector<unsigned long long> divideFile(string, int&);
int divideFile(string, int&, vector<string>&);
vector<unsigned long long> setFilePosEachLine(string, int&);
void splitAtDash(string&, set<string>&);
void splitAtDash(string&, vector<string>&);
void splitAtChar(string&, vector<string>&, char);
+ void splitAtChar(string&, string&, char);
int removeConfidences(string&);
//math operation
int getRandomIndex(int); //highest
int control_pressed;
- bool executing, runParse, jumble, gui;
+ bool executing, runParse, jumble, gui, mothurCalling;
//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 getAccnosFile() { return accnosfile; }
string getTaxonomyFile() { return taxonomyfile; }
string getFlowFile() { return flowfile; }
+ string getBiomFile() { return biomfile; }
string getProcessors() { return processors; }
void setListFile(string f) { listfile = getFullPathName(f); }
void setAccnosFile(string f) { accnosfile = getFullPathName(f); }
void setTaxonomyFile(string f) { taxonomyfile = getFullPathName(f); }
void setFlowFile(string f) { flowfile = getFullPathName(f); }
+ void setBiomFile(string f) { biomfile = getFullPathName(f); }
void setProcessors(string p) { processors = p; }
void printCurrentFiles();
taxonomyfile = "";
processors = "1";
flowfile = "";
+ biomfile = "";
gui = false;
printedHeaders = false;
commandInputsConvertError = false;
+ mothurCalling = false;
sharedHeaderMode = "";
}
~MothurOut();
string defaultPath, outputDir;
string releaseDate, version;
- string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
+ string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
vector<string> Groups;