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);
30 string getOutputDir() { return outputDir; }
31 void setOutputDir(string);
33 string getReleaseDate() { return releaseDate; }
34 void setReleaseDate(string r) { releaseDate = r; }
35 string getVersion() { return version; }
36 void setVersion(string r) { version = r; }
38 //functions from mothur.h
40 vector<unsigned long int> divideFile(string, int&);
41 vector<unsigned long int> setFilePosEachLine(string, int&);
42 vector<unsigned long int> setFilePosFasta(string, int&);
43 string sortFile(string, string);
44 void appendFiles(string, string);
45 int renameFile(string, string); //oldname, newname
46 string getFullPathName(string);
47 string hasPath(string);
48 string getExtension(string);
49 string getPathName(string);
50 string getSimpleName(string);
51 string getRootName(string);
53 int openOutputFile(string, ofstream&);
54 int openOutputFileAppend(string, ofstream&);
55 int openInputFile(string, ifstream&);
56 int openInputFile(string, ifstream&, string); //no error given
57 string getline(ifstream&);
58 string getline(istringstream&);
59 void gobble(istream&);
60 void gobble(istringstream&);
63 bool checkReleaseVersion(ifstream&, string);
64 bool anyLabelsToProcess(string, set<string>&, string);
65 bool inUsersGroups(vector<string>, vector<string>);
66 bool inUsersGroups(string, vector<string>);
67 void getNumSeqs(ifstream&, int&);
68 int getNumSeqs(ifstream&);
69 int getNumNames(string);
74 void splitAtEquals(string&, string&);
75 void splitAtComma(string&, string&);
76 void splitAtComma(string&, vector<string>&);
77 void splitAtDash(string&, set<int>&);
78 void splitAtDash(string&, set<string>&);
79 void splitAtDash(string&, vector<string>&);
80 void splitAtChar(string&, vector<string>&, char);
83 int factorial(int num);
84 vector<vector<double> > binomial(int);
85 float ceilDist(float, int);
86 float roundDist(float, int);
93 static MothurOut* _uniqueInstance;
94 MothurOut( const MothurOut& ); // Disable copy constructor
95 void operator=( const MothurOut& ); // Disable assignment operator
96 MothurOut() { control_pressed = false; defaultPath=""; };
100 string defaultPath, outputDir;
101 string releaseDate, version;
105 int mem_usage(double&, double&);
108 /***********************************************/