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
  18 class MothurOut {
  19
  20         public:
  21                 static MothurOut* getInstance();
  22                 void setFileName(string);
  23
  24                 void mothurOut(string);
  25                 void mothurOutEndLine();
  26                 void mothurOutJustToLog(string);
  27                 void errorOut(exception&, string, string);
  28                 void closeLog();
  29                 string getDefaultPath() { return defaultPath; }
  30                 void setDefaultPath(string);
  31                 string getOutputDir() { return outputDir; }
  32                 void setOutputDir(string);
  33
  34                 string getReleaseDate() { return releaseDate; }
  35                 void setReleaseDate(string r) { releaseDate = r; }
  36                 string getVersion() { return version; }
  37                 void setVersion(string r) { version = r; }
  38
  39                 //functions from mothur.h
  40                 //file operations
  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);
  53                 bool isBlank(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);
  63
  64                 //searchs and checks
  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);
  72                 bool isTrue(string);
  73
  74
  75                 //string manipulation
  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);
  83
  84                 //math operation
  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);
  90
  91                 int control_pressed;
  92                 bool executing;
  93
  94                 //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
  95                 string getPhylipFile()          { return phylipfile;            }
  96                 string getColumnFile()          { return columnfile;            }
  97                 string getListFile()            { return listfile;                      }
  98                 string getRabundFile()          { return rabundfile;            }
  99                 string getSabundFile()          { return sabundfile;            }
 100                 string getNameFile()            { return namefile;                      }
 101                 string getGroupFile()           { return groupfile;                     }
 102                 string getOrderFile()           { return orderfile;                     }
 103                 string getOrderGroupFile()      { return ordergroupfile;        }
 104                 string getTreeFile()            { return treefile;                      }
 105                 string getSharedFile()          { return sharedfile;            }
 106                 string getRelAbundFile()        { return relabundfile;          }
 107                 string getDesignFile()          { return designfile;            }
 108                 string getFastaFile()           { return fastafile;                     }
 109                 string getSFFFile()                     { return sfffile;                       }
 110                 string getQualFile()            { return qualfile;                      }
 111                 string getOligosFile()          { return oligosfile;            }
 112                 string getAccnosFile()          { return accnosfile;            }
 113                 string getTaxonomyFile()        { return taxonomyfile;          }
 114
 115                 void setListFile(string f)                      { listfile = getFullPathName(f);                        }
 116                 void setTreeFile(string f)                      { treefile = getFullPathName(f);                        }
 117                 void setGroupFile(string f)                     { groupfile = getFullPathName(f);                       }
 118                 void setPhylipFile(string f)            { phylipfile = getFullPathName(f);                      }
 119                 void setColumnFile(string f)            { columnfile = getFullPathName(f);                      }
 120                 void setNameFile(string f)                      { namefile = getFullPathName(f);                        }
 121                 void setRabundFile(string f)            { rabundfile = getFullPathName(f);                      }
 122                 void setSabundFile(string f)            { sabundfile = getFullPathName(f);                      }
 123                 void setSharedFile(string f)            { sharedfile = getFullPathName(f);                      }
 124                 void setRelAbundFile(string f)          { relabundfile = getFullPathName(f);            }
 125                 void setOrderFile(string f)                     { orderfile = getFullPathName(f);                       }
 126                 void setOrderGroupFile(string f)        { ordergroupfile = getFullPathName(f);          }
 127                 void setDesignFile(string f)            { designfile = getFullPathName(f);                      }
 128                 void setFastaFile(string f)                     { fastafile = getFullPathName(f);                       }
 129                 void setSFFFile(string f)                       { sfffile = getFullPathName(f);                         }
 130                 void setQualFile(string f)                      { qualfile = getFullPathName(f);                        }
 131                 void setOligosFile(string f)            { oligosfile = getFullPathName(f);                      }
 132                 void setAccnosFile(string f)            { accnosfile = getFullPathName(f);                      }
 133                 void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
 134
 135                 void printCurrentFiles();
 136                 void clearCurrentFiles();
 137
 138         private:
 139                 static MothurOut* _uniqueInstance;
 140                 MothurOut( const MothurOut& ); // Disable copy constructor
 141                 void operator=( const MothurOut& ); // Disable assignment operator
 142                 MothurOut() {
 143                         control_pressed = false; defaultPath="";
 144                         phylipfile = "";
 145                         columnfile = "";
 146                         listfile = "";
 147                         rabundfile = "";
 148                         sabundfile = "";
 149                         namefile = "";
 150                         groupfile = "";
 151                         designfile = "";
 152                         orderfile = "";
 153                         treefile = "";
 154                         sharedfile = "";
 155                         ordergroupfile = "";
 156                         relabundfile = "";
 157                         fastafile = "";
 158                         qualfile = "";
 159                         sfffile = "";
 160                         oligosfile = "";
 161                         accnosfile = "";
 162                         taxonomyfile = "";
 163                 };
 164                 ~MothurOut();
 165
 166                 string logFileName;
 167                 string defaultPath, outputDir;
 168                 string releaseDate, version;
 169
 170                 string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
 171                 string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile;
 172
 173
 174                 ofstream out;
 175
 176                 int mem_usage(double&, double&);
 177
 178 };
 179 /***********************************************/
 180
 181 #endif
 182