8 * Created by westcott on 2/25/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
15 /***********************************************/
20 static MothurOut* getInstance();
21 void setFileName(string);
23 void mothurOut(string);
24 void mothurOutEndLine();
25 void mothurOutJustToLog(string);
26 void errorOut(exception&, string, string);
28 string getDefaultPath() { return defaultPath; }
29 void setDefaultPath(string);
31 string getReleaseDate() { return releaseDate; }
32 void setReleaseDate(string r) { releaseDate = r; }
33 string getVersion() { return version; }
34 void setVersion(string r) { version = r; }
36 //functions from mothur.h
38 vector<unsigned long int> divideFile(string, int&);
39 vector<unsigned long int> setFilePosEachLine(string, int&);
40 vector<unsigned long int> setFilePosFasta(string, int&);
41 string sortFile(string, string);
42 void appendFiles(string, string);
43 int renameFile(string, string); //oldname, newname
44 string getFullPathName(string);
45 string hasPath(string);
46 string getExtension(string);
47 string getPathName(string);
48 string getSimpleName(string);
49 string getRootName(string);
51 int openOutputFile(string, ofstream&);
52 int openOutputFileAppend(string, ofstream&);
53 int openInputFile(string, ifstream&);
54 int openInputFile(string, ifstream&, string); //no error given
55 string getline(ifstream&);
56 string getline(istringstream&);
57 void gobble(istream&);
58 void gobble(istringstream&);
61 bool checkReleaseVersion(ifstream&, string);
62 bool anyLabelsToProcess(string, set<string>&, string);
63 bool inUsersGroups(vector<string>, vector<string>);
64 bool inUsersGroups(string, vector<string>);
65 void getNumSeqs(ifstream&, int&);
66 int getNumSeqs(ifstream&);
67 int getNumNames(string);
72 void splitAtEquals(string&, string&);
73 void splitAtComma(string&, string&);
74 void splitAtComma(string&, vector<string>&);
75 void splitAtDash(string&, set<int>&);
76 void splitAtDash(string&, set<string>&);
77 void splitAtDash(string&, vector<string>&);
78 void splitAtChar(string&, vector<string>&, char);
81 int factorial(int num);
82 vector<vector<double> > binomial(int);
83 float ceilDist(float, int);
84 float roundDist(float, int);
91 static MothurOut* _uniqueInstance;
92 MothurOut( const MothurOut& ); // Disable copy constructor
93 void operator=( const MothurOut& ); // Disable assignment operator
94 MothurOut() { control_pressed = false; defaultPath=""; };
99 string releaseDate, version;
103 int mem_usage(double&, double&);
106 /***********************************************/