8 * Created by westcott on 2/25/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
16 /***********************************************/
21 static MothurOut* getInstance();
22 void setFileName(string);
24 void mothurOut(string);
25 void mothurOutEndLine();
26 void mothurOutJustToLog(string);
27 void errorOut(exception&, string, string);
29 string getDefaultPath() { return defaultPath; }
30 void setDefaultPath(string);
31 string getOutputDir() { return outputDir; }
32 void setOutputDir(string);
34 string getReleaseDate() { return releaseDate; }
35 void setReleaseDate(string r) { releaseDate = r; }
36 string getVersion() { return version; }
37 void setVersion(string r) { version = r; }
39 //functions from mothur.h
41 vector<unsigned long int> divideFile(string, int&);
42 vector<unsigned long int> setFilePosEachLine(string, int&);
43 vector<unsigned long int> setFilePosFasta(string, int&);
44 string sortFile(string, string);
45 void appendFiles(string, string);
46 int renameFile(string, string); //oldname, newname
47 string getFullPathName(string);
48 string hasPath(string);
49 string getExtension(string);
50 string getPathName(string);
51 string getSimpleName(string);
52 string getRootName(string);
54 int openOutputFile(string, ofstream&);
55 int openOutputFileAppend(string, ofstream&);
56 int openInputFile(string, ifstream&);
57 int openInputFile(string, ifstream&, string); //no error given
58 string getline(ifstream&);
59 string getline(istringstream&);
60 void gobble(istream&);
61 void gobble(istringstream&);
62 map<string, int> readNames(string);
65 bool checkReleaseVersion(ifstream&, string);
66 bool anyLabelsToProcess(string, set<string>&, string);
67 bool inUsersGroups(vector<string>, vector<string>);
68 bool inUsersGroups(string, vector<string>);
69 void getNumSeqs(ifstream&, int&);
70 int getNumSeqs(ifstream&);
71 int getNumNames(string);
76 void splitAtEquals(string&, string&);
77 void splitAtComma(string&, string&);
78 void splitAtComma(string&, vector<string>&);
79 void splitAtDash(string&, set<int>&);
80 void splitAtDash(string&, set<string>&);
81 void splitAtDash(string&, vector<string>&);
82 void splitAtChar(string&, vector<string>&, char);
85 int factorial(int num);
86 vector<vector<double> > binomial(int);
87 float ceilDist(float, int);
88 float roundDist(float, int);
89 unsigned int fromBase36(string);
95 static MothurOut* _uniqueInstance;
96 MothurOut( const MothurOut& ); // Disable copy constructor
97 void operator=( const MothurOut& ); // Disable assignment operator
98 MothurOut() { control_pressed = false; defaultPath=""; };
102 string defaultPath, outputDir;
103 string releaseDate, version;
107 int mem_usage(double&, double&);
110 /***********************************************/