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 mothurOutJustToScreen(string); //writes to cout
void mothurOutJustToLog(string);
void errorOut(exception&, string, string);
void closeLog();
vector<string> binLabelsInFile;
vector<string> currentBinLabels;
string saveNextLabel, argv, sharedHeaderMode, groupMode;
- bool printedHeaders, commandInputsConvertError;
+ bool printedHeaders, commandInputsConvertError, changedSeqNames;
//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&);
+ vector<unsigned long long> divideFile(string, int&); //divides splitting unevenness by sequence
+ vector<unsigned long long> divideFilePerLine(string, int&); //divides splitting unevenness at line breaks
int divideFile(string, int&, vector<string>&);
vector<unsigned long long> setFilePosEachLine(string, int&);
vector<unsigned long long> setFilePosFasta(string, int&);
string sortFile(string, string);
int appendFiles(string, string);
+ int appendFilesWithoutHeaders(string, string);
int renameFile(string, string); //oldname, newname
string getFullPathName(string);
string findProgramPath(string programName);
set<string> readAccnos(string);
int readAccnos(string, vector<string>&);
map<string, int> readNames(string);
+ map<string, int> readNames(string, unsigned long int&);
int readTax(string, map<string, string>&);
int readNames(string, map<string, string>&, map<string, int>&);
int readNames(string, map<string, string>&);
string removeQuotes(string);
string makeList(vector<string>&);
bool isSubset(vector<string>, vector<string>); //bigSet, subset
+ int checkName(string&);
//math operation
int factorial(int num);
vector<double> getStandardDeviation(vector< vector<double> >&);
vector<double> getStandardDeviation(vector< vector<double> >&, vector<double>&);
vector<double> getAverages(vector< vector<double> >&);
+ vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&);
+ vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&, vector< vector<seqDist> >&);
+ vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&, string);
+ vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&);
int control_pressed;
bool executing, runParse, jumble, gui, mothurCalling, debug;
- //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes.
+ //current files - if you add a new type you must edit optionParser->getParameters, get.current and set.current commands and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes. add a get and set function.
string getPhylipFile() { return phylipfile; }
string getColumnFile() { return columnfile; }
string getListFile() { return listfile; }
string getFlowFile() { return flowfile; }
string getBiomFile() { return biomfile; }
string getCountTableFile() { return counttablefile; }
+ string getSummaryFile() { return summaryfile; }
string getProcessors() { return processors; }
void setListFile(string f) { listfile = getFullPathName(f); }
void setTaxonomyFile(string f) { taxonomyfile = getFullPathName(f); }
void setFlowFile(string f) { flowfile = getFullPathName(f); }
void setBiomFile(string f) { biomfile = getFullPathName(f); }
+ void setSummaryFile(string f) { summaryfile = getFullPathName(f); }
void setCountTableFile(string f) { counttablefile = getFullPathName(f); groupMode = "count"; }
void setProcessors(string p) { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n"); }
flowfile = "";
biomfile = "";
counttablefile = "";
+ summaryfile = "";
gui = false;
printedHeaders = false;
commandInputsConvertError = false;
debug = false;
sharedHeaderMode = "";
groupMode = "group";
+ changedSeqNames = false;
}
~MothurOut();
string releaseDate, version;
string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
- string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile;
+ string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile, summaryfile;
vector<string> Groups;
vector<string> namesOfGroups;