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); //writes to cout and the logfile
  24                 void mothurOutEndLine(); //writes to cout and the logfile
  25                 void mothurOut(string, ofstream&); //writes to the ofstream, cout and the logfile
  26                 void mothurOutEndLine(ofstream&); //writes to the ofstream, cout and the logfile
  27                 void mothurOutJustToLog(string);
  28                 void errorOut(exception&, string, string);
  29                 void closeLog();
  30                 string getDefaultPath() { return defaultPath; }
  31                 void setDefaultPath(string);
  32                 string getOutputDir() { return outputDir; }
  33                 void setOutputDir(string);
  34
  35                 string getReleaseDate() { return releaseDate; }
  36                 void setReleaseDate(string r) { releaseDate = r; }
  37                 string getVersion() { return version; }
  38                 void setVersion(string r) { version = r; }
  39                 vector<string> Groups;
  40                 vector<string> Treenames;
  41                 map<string, string> names;
  42                 vector<string> namesOfGroups;
  43                 vector<string> binLabelsInFile;
  44                 vector<string> currentBinLabels;
  45                 string saveNextLabel, argv, sharedHeaderMode;
  46                 bool printedHeaders;
  47
  48                 //functions from mothur.h
  49                 //file operations
  50                 vector<unsigned long int> divideFile(string, int&);
  51                 int divideFile(string, int&, vector<string>&);
  52                 vector<unsigned long int> setFilePosEachLine(string, int&);
  53                 vector<unsigned long int> setFilePosFasta(string, int&);
  54                 string sortFile(string, string);
  55                 void appendFiles(string, string);
  56                 int renameFile(string, string); //oldname, newname
  57                 string getFullPathName(string);
  58                 string hasPath(string);
  59                 string getExtension(string);
  60                 string getPathName(string);
  61                 string getSimpleName(string);
  62                 string getRootName(string);
  63                 bool isBlank(string);
  64                 int openOutputFile(string, ofstream&);
  65                 int openOutputFileAppend(string, ofstream&);
  66                 int openInputFile(string, ifstream&);
  67                 int openInputFile(string, ifstream&, string); //no error given
  68                 string getline(ifstream&);
  69                 string getline(istringstream&);
  70                 void gobble(istream&);
  71                 void gobble(istringstream&);
  72                 map<string, int> readNames(string);
  73                 int readNames(string, map<string, string>&);
  74                 int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
  75                 void mothurRemove(string);
  76
  77                 //searchs and checks
  78                 bool checkReleaseVersion(ifstream&, string);
  79                 bool anyLabelsToProcess(string, set<string>&, string);
  80                 bool inUsersGroups(vector<string>, vector<string>);
  81                 bool inUsersGroups(string, vector<string>);
  82                 void getNumSeqs(ifstream&, int&);
  83                 int getNumSeqs(ifstream&);
  84                 int getNumNames(string);
  85                 bool isTrue(string);
  86                 bool isContainingOnlyDigits(string);
  87
  88
  89                 //string manipulation
  90                 void splitAtEquals(string&, string&);
  91                 void splitAtComma(string&, string&);
  92                 void splitAtComma(string&, vector<string>&);
  93                 void splitAtDash(string&, set<int>&);
  94                 void splitAtDash(string&, set<string>&);
  95                 void splitAtDash(string&, vector<string>&);
  96                 void splitAtChar(string&, vector<string>&, char);
  97
  98                 //math operation
  99                 int factorial(int num);
 100                 vector<vector<double> > binomial(int);
 101                 float ceilDist(float, int);
 102                 float roundDist(float, int);
 103                 unsigned int fromBase36(string);
 104                 int getRandomIndex(int); //highest
 105
 106                 int control_pressed;
 107                 bool executing, runParse, jumble, gui;
 108
 109                 //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
 110                 string getPhylipFile()          { return phylipfile;            }
 111                 string getColumnFile()          { return columnfile;            }
 112                 string getListFile()            { return listfile;                      }
 113                 string getRabundFile()          { return rabundfile;            }
 114                 string getSabundFile()          { return sabundfile;            }
 115                 string getNameFile()            { return namefile;                      }
 116                 string getGroupFile()           { return groupfile;                     }
 117                 string getOrderFile()           { return orderfile;                     }
 118                 string getOrderGroupFile()      { return ordergroupfile;        }
 119                 string getTreeFile()            { return treefile;                      }
 120                 string getSharedFile()          { return sharedfile;            }
 121                 string getRelAbundFile()        { return relabundfile;          }
 122                 string getDesignFile()          { return designfile;            }
 123                 string getFastaFile()           { return fastafile;                     }
 124                 string getSFFFile()                     { return sfffile;                       }
 125                 string getQualFile()            { return qualfile;                      }
 126                 string getOligosFile()          { return oligosfile;            }
 127                 string getAccnosFile()          { return accnosfile;            }
 128                 string getTaxonomyFile()        { return taxonomyfile;          }
 129                 string getFlowFile()            { return flowfile;                      }
 130                 string getProcessors()          { return processors;            }
 131
 132                 void setListFile(string f)                      { listfile = getFullPathName(f);                        }
 133                 void setTreeFile(string f)                      { treefile = getFullPathName(f);                        }
 134                 void setGroupFile(string f)                     { groupfile = getFullPathName(f);                       }
 135                 void setPhylipFile(string f)            { phylipfile = getFullPathName(f);                      }
 136                 void setColumnFile(string f)            { columnfile = getFullPathName(f);                      }
 137                 void setNameFile(string f)                      { namefile = getFullPathName(f);                        }
 138                 void setRabundFile(string f)            { rabundfile = getFullPathName(f);                      }
 139                 void setSabundFile(string f)            { sabundfile = getFullPathName(f);                      }
 140                 void setSharedFile(string f)            { sharedfile = getFullPathName(f);                      }
 141                 void setRelAbundFile(string f)          { relabundfile = getFullPathName(f);            }
 142                 void setOrderFile(string f)                     { orderfile = getFullPathName(f);                       }
 143                 void setOrderGroupFile(string f)        { ordergroupfile = getFullPathName(f);          }
 144                 void setDesignFile(string f)            { designfile = getFullPathName(f);                      }
 145                 void setFastaFile(string f)                     { fastafile = getFullPathName(f);                       }
 146                 void setSFFFile(string f)                       { sfffile = getFullPathName(f);                         }
 147                 void setQualFile(string f)                      { qualfile = getFullPathName(f);                        }
 148                 void setOligosFile(string f)            { oligosfile = getFullPathName(f);                      }
 149                 void setAccnosFile(string f)            { accnosfile = getFullPathName(f);                      }
 150                 void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
 151                 void setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
 152                 void setProcessors(string p)            { processors = p;                                                       }
 153
 154                 void printCurrentFiles();
 155                 bool hasCurrentFiles();
 156                 void clearCurrentFiles();
 157
 158         private:
 159                 static MothurOut* _uniqueInstance;
 160                 MothurOut( const MothurOut& ); // Disable copy constructor
 161                 void operator=( const MothurOut& ); // Disable assignment operator
 162                 MothurOut() {
 163                         control_pressed = false; defaultPath="";
 164                         phylipfile = "";
 165                         columnfile = "";
 166                         listfile = "";
 167                         rabundfile = "";
 168                         sabundfile = "";
 169                         namefile = "";
 170                         groupfile = "";
 171                         designfile = "";
 172                         orderfile = "";
 173                         treefile = "";
 174                         sharedfile = "";
 175                         ordergroupfile = "";
 176                         relabundfile = "";
 177                         fastafile = "";
 178                         qualfile = "";
 179                         sfffile = "";
 180                         oligosfile = "";
 181                         accnosfile = "";
 182                         taxonomyfile = "";
 183                         processors = "1";
 184                         flowfile = "";
 185                         gui = false;
 186                         printedHeaders = false;
 187                         sharedHeaderMode = "";
 188                 }
 189                 ~MothurOut();
 190
 191                 string logFileName;
 192                 string defaultPath, outputDir;
 193                 string releaseDate, version;
 194
 195                 string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
 196                 string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 197
 198
 199                 ofstream out;
 200
 201                 int mem_usage(double&, double&);
 202
 203 };
 204 /***********************************************/
 205
 206 #endif
 207