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
  40                 void addGroup(string g) { Groups.push_back(g); }
  41                 void setGroups(vector<string>& g) { sort(g.begin(), g.end()); Groups = g; }
  42                 void clearGroups() { Groups.clear(); }
  43             int getNumGroups() { return Groups.size(); }
  44                 vector<string> getGroups() { sort(Groups.begin(), Groups.end()); return Groups; }
  45                 void addAllGroup(string g) { namesOfGroups.push_back(g); }
  46                 void setAllGroups(vector<string>& g) { sort(g.begin(), g.end()); namesOfGroups = g; }
  47                 void clearAllGroups() { namesOfGroups.clear(); }
  48                 int getNumAllGroups() { return namesOfGroups.size(); }
  49
  50                 vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
  51                 vector<string> Treenames;
  52                 map<string, string> names;
  53                 vector<string> binLabelsInFile;
  54                 vector<string> currentBinLabels;
  55                 string saveNextLabel, argv, sharedHeaderMode;
  56                 bool printedHeaders;
  57
  58                 //functions from mothur.h
  59                 //file operations
  60                 vector<unsigned long long> divideFile(string, int&);
  61                 int divideFile(string, int&, vector<string>&);
  62                 vector<unsigned long long> setFilePosEachLine(string, int&);
  63                 vector<unsigned long long> setFilePosFasta(string, int&);
  64                 string sortFile(string, string);
  65                 int appendFiles(string, string);
  66                 int renameFile(string, string); //oldname, newname
  67                 string getFullPathName(string);
  68                 string hasPath(string);
  69                 string getExtension(string);
  70                 string getPathName(string);
  71                 string getSimpleName(string);
  72                 string getRootName(string);
  73                 bool isBlank(string);
  74                 int openOutputFile(string, ofstream&);
  75                 int openOutputFileAppend(string, ofstream&);
  76                 int openInputFile(string, ifstream&);
  77                 int openInputFile(string, ifstream&, string); //no error given
  78                 string getline(ifstream&);
  79                 string getline(istringstream&);
  80                 void gobble(istream&);
  81                 void gobble(istringstream&);
  82                 map<string, int> readNames(string);
  83                 int readNames(string, map<string, string>&);
  84                 int readNames(string, map<string, vector<string> >&);
  85                 int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
  86                 int mothurRemove(string);
  87
  88
  89                 //searchs and checks
  90                 bool checkReleaseVersion(ifstream&, string);
  91                 bool anyLabelsToProcess(string, set<string>&, string);
  92                 bool inUsersGroups(vector<string>, vector<string>);
  93                 bool inUsersGroups(string, vector<string>);
  94                 void getNumSeqs(ifstream&, int&);
  95                 int getNumSeqs(ifstream&);
  96                 int getNumNames(string);
  97                 int getNumChar(string, char);
  98                 bool isTrue(string);
  99                 bool isContainingOnlyDigits(string);
 100
 101
 102                 //string manipulation
 103                 void splitAtEquals(string&, string&);
 104                 void splitAtComma(string&, string&);
 105                 void splitAtComma(string&, vector<string>&);
 106                 void splitAtDash(string&, set<int>&);
 107                 void splitAtDash(string&, set<string>&);
 108                 void splitAtDash(string&, vector<string>&);
 109                 void splitAtChar(string&, vector<string>&, char);
 110                 int removeConfidences(string&);
 111
 112                 //math operation
 113                 int factorial(int num);
 114                 vector<vector<double> > binomial(int);
 115                 float ceilDist(float, int);
 116                 float roundDist(float, int);
 117                 unsigned int fromBase36(string);
 118                 int getRandomIndex(int); //highest
 119
 120                 int control_pressed;
 121                 bool executing, runParse, jumble, gui;
 122
 123                 //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
 124                 string getPhylipFile()          { return phylipfile;            }
 125                 string getColumnFile()          { return columnfile;            }
 126                 string getListFile()            { return listfile;                      }
 127                 string getRabundFile()          { return rabundfile;            }
 128                 string getSabundFile()          { return sabundfile;            }
 129                 string getNameFile()            { return namefile;                      }
 130                 string getGroupFile()           { return groupfile;                     }
 131                 string getOrderFile()           { return orderfile;                     }
 132                 string getOrderGroupFile()      { return ordergroupfile;        }
 133                 string getTreeFile()            { return treefile;                      }
 134                 string getSharedFile()          { return sharedfile;            }
 135                 string getRelAbundFile()        { return relabundfile;          }
 136                 string getDesignFile()          { return designfile;            }
 137                 string getFastaFile()           { return fastafile;                     }
 138                 string getSFFFile()                     { return sfffile;                       }
 139                 string getQualFile()            { return qualfile;                      }
 140                 string getOligosFile()          { return oligosfile;            }
 141                 string getAccnosFile()          { return accnosfile;            }
 142                 string getTaxonomyFile()        { return taxonomyfile;          }
 143                 string getFlowFile()            { return flowfile;                      }
 144                 string getProcessors()          { return processors;            }
 145
 146                 void setListFile(string f)                      { listfile = getFullPathName(f);                        }
 147                 void setTreeFile(string f)                      { treefile = getFullPathName(f);                        }
 148                 void setGroupFile(string f)                     { groupfile = getFullPathName(f);                       }
 149                 void setPhylipFile(string f)            { phylipfile = getFullPathName(f);                      }
 150                 void setColumnFile(string f)            { columnfile = getFullPathName(f);                      }
 151                 void setNameFile(string f)                      { namefile = getFullPathName(f);                        }
 152                 void setRabundFile(string f)            { rabundfile = getFullPathName(f);                      }
 153                 void setSabundFile(string f)            { sabundfile = getFullPathName(f);                      }
 154                 void setSharedFile(string f)            { sharedfile = getFullPathName(f);                      }
 155                 void setRelAbundFile(string f)          { relabundfile = getFullPathName(f);            }
 156                 void setOrderFile(string f)                     { orderfile = getFullPathName(f);                       }
 157                 void setOrderGroupFile(string f)        { ordergroupfile = getFullPathName(f);          }
 158                 void setDesignFile(string f)            { designfile = getFullPathName(f);                      }
 159                 void setFastaFile(string f)                     { fastafile = getFullPathName(f);                       }
 160                 void setSFFFile(string f)                       { sfffile = getFullPathName(f);                         }
 161                 void setQualFile(string f)                      { qualfile = getFullPathName(f);                        }
 162                 void setOligosFile(string f)            { oligosfile = getFullPathName(f);                      }
 163                 void setAccnosFile(string f)            { accnosfile = getFullPathName(f);                      }
 164                 void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
 165                 void setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
 166                 void setProcessors(string p)            { processors = p;                                                       }
 167
 168                 void printCurrentFiles();
 169                 bool hasCurrentFiles();
 170                 void clearCurrentFiles();
 171
 172         private:
 173                 static MothurOut* _uniqueInstance;
 174                 MothurOut( const MothurOut& ); // Disable copy constructor
 175                 void operator=( const MothurOut& ); // Disable assignment operator
 176                 MothurOut() {
 177                         control_pressed = false; defaultPath="";
 178                         phylipfile = "";
 179                         columnfile = "";
 180                         listfile = "";
 181                         rabundfile = "";
 182                         sabundfile = "";
 183                         namefile = "";
 184                         groupfile = "";
 185                         designfile = "";
 186                         orderfile = "";
 187                         treefile = "";
 188                         sharedfile = "";
 189                         ordergroupfile = "";
 190                         relabundfile = "";
 191                         fastafile = "";
 192                         qualfile = "";
 193                         sfffile = "";
 194                         oligosfile = "";
 195                         accnosfile = "";
 196                         taxonomyfile = "";
 197                         processors = "1";
 198                         flowfile = "";
 199                         gui = false;
 200                         printedHeaders = false;
 201                         sharedHeaderMode = "";
 202                 }
 203                 ~MothurOut();
 204
 205                 string logFileName;
 206                 string defaultPath, outputDir;
 207                 string releaseDate, version;
 208
 209                 string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile;
 210                 string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
 211
 212                 vector<string> Groups;
 213                 vector<string> namesOfGroups;
 214                 ofstream out;
 215
 216                 int mem_usage(double&, double&);
 217
 218 };
 219 /***********************************************/
 220
 221 #endif
 222