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 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();
void mothurOutJustToLog(string);
void errorOut(exception&, string, string);
void closeLog();
vector<string> binLabelsInFile;
vector<string> currentBinLabels;
string saveNextLabel, argv, sharedHeaderMode, groupMode;
vector<string> binLabelsInFile;
vector<string> currentBinLabels;
string saveNextLabel, argv, sharedHeaderMode, groupMode;
//functions from mothur.h
//file operations
bool dirCheck(string&); //completes path, appends appropriate / or \, makes sure dir is writable.
//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 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 renameFile(string, string); //oldname, newname
string getFullPathName(string);
string findProgramPath(string programName);
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);
set<string> readAccnos(string);
int readAccnos(string, vector<string>&);
map<string, int> readNames(string);
int readNames(string, map<string, string>&, map<string, int>&);
int readNames(string, map<string, string>&);
int readNames(string, map<string, string>&, bool);
int readNames(string, map<string, string>&, map<string, int>&);
int readNames(string, map<string, string>&);
int readNames(string, map<string, string>&, bool);
string removeQuotes(string);
string makeList(vector<string>&);
bool isSubset(vector<string>, vector<string>); //bigSet, subset
string removeQuotes(string);
string makeList(vector<string>&);
bool isSubset(vector<string>, vector<string>); //bigSet, subset
vector<double> getStandardDeviation(vector< vector<double> >&);
vector<double> getStandardDeviation(vector< vector<double> >&, vector<double>&);
vector<double> getAverages(vector< vector<double> >&);
vector<double> getStandardDeviation(vector< vector<double> >&);
vector<double> getStandardDeviation(vector< vector<double> >&, vector<double>&);
vector<double> getAverages(vector< vector<double> >&);
+ double getAverage(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;
int control_pressed;
bool executing, runParse, jumble, gui, mothurCalling, debug;
string getPhylipFile() { return phylipfile; }
string getColumnFile() { return columnfile; }
string getListFile() { return listfile; }
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 getFlowFile() { return flowfile; }
string getBiomFile() { return biomfile; }
string getCountTableFile() { return counttablefile; }
string getProcessors() { return processors; }
void setListFile(string f) { listfile = getFullPathName(f); }
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 setTaxonomyFile(string f) { taxonomyfile = getFullPathName(f); }
void setFlowFile(string f) { flowfile = getFullPathName(f); }
void setBiomFile(string f) { biomfile = getFullPathName(f); }
void setCountTableFile(string f) { counttablefile = getFullPathName(f); groupMode = "count"; }
void setProcessors(string p) { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n"); }
void setCountTableFile(string f) { counttablefile = getFullPathName(f); groupMode = "count"; }
void setProcessors(string p) { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n"); }
string releaseDate, version;
string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
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;