mothurout.h

   1 #ifndef MOTHUROUT_H
   2 #define MOTHUROUT_H
   3
   4 /*
   5  *  mothurOut.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 2/25/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14
  15 /***********************************************/
  16
  17 class MothurOut {
  18
  19         public:
  20                 static MothurOut* getInstance();
  21                 void setFileName(string);
  22
  23                 void mothurOut(string);
  24                 void mothurOutEndLine();
  25                 void mothurOutJustToLog(string);
  26                 void errorOut(exception&, string, string);
  27                 void closeLog();
  28                 string getDefaultPath() { return defaultPath; }
  29                 void setDefaultPath(string);
  30                 string getOutputDir() { return outputDir; }
  31                 void setOutputDir(string);
  32
  33                 string getReleaseDate() { return releaseDate; }
  34                 void setReleaseDate(string r) { releaseDate = r; }
  35                 string getVersion() { return version; }
  36                 void setVersion(string r) { version = r; }
  37
  38                 //functions from mothur.h
  39                 //file operations
  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);
  52                 bool isBlank(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&);
  61
  62                 //searchs and checks
  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);
  70                 bool isTrue(string);
  71
  72
  73                 //string manipulation
  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);
  81
  82                 //math operation
  83                 int factorial(int num);
  84                 vector<vector<double> > binomial(int);
  85                 float ceilDist(float, int);
  86                 float roundDist(float, int);
  87
  88                 int control_pressed;
  89                 bool executing;
  90
  91
  92         private:
  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=""; };
  97                 ~MothurOut();
  98
  99                 string logFileName;
 100                 string defaultPath, outputDir;
 101                 string releaseDate, version;
 102
 103                 ofstream out;
 104
 105                 int mem_usage(double&, double&);
 106
 107 };
 108 /***********************************************/
 109
 110 #endif
 111