mothur.cpp

   1 /*
   2  *  interface.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 8/14/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "mothur.h"
  11 #include "engine.hpp"
  12 #include "globaldata.hpp"
  13
  14 /**************************************************************************************************/
  15
  16 GlobalData* GlobalData::_uniqueInstance = 0;
  17 CommandFactory* CommandFactory::_uniqueInstance = 0;
  18
  19 int main(int argc, char *argv[]){
  20         try {
  21
  22                 //remove old logfile
  23 //              string log = "mothur.logFile";
  24 //              remove(log.c_str());
  25
  26                 time_t ltime = time(NULL); /* calendar time */
  27                 string logFileName = "mothur." + toString(ltime) + ".logfile";
  28
  29                 //version
  30                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  31                         system("clear");
  32                         #if defined (__APPLE__) || (__MACH__)
  33                                 mothurOutJustToLog("Mac version");
  34                                 mothurOutEndLine(); mothurOutEndLine();
  35                         #else
  36                                 mothurOutJustToLog("Linux version");
  37                                 mothurOutEndLine(); mothurOutEndLine();
  38                         #endif
  39
  40                 #else
  41                         system("CLS");
  42                         mothurOutJustToLog("Windows version");
  43                         mothurOutEndLine(); mothurOutEndLine();
  44                 #endif
  45
  46
  47                 //header
  48                 mothurOut("mothur v.1.7.2");
  49                 mothurOutEndLine();
  50                 mothurOut("Last updated: 12/04/2009");
  51                 mothurOutEndLine();
  52                 mothurOutEndLine();
  53                 mothurOut("by");
  54                 mothurOutEndLine();
  55                 mothurOut("Patrick D. Schloss");
  56                 mothurOutEndLine();
  57                 mothurOutEndLine();
  58                 mothurOut("Department of Microbiology & Immunology");
  59                 mothurOutEndLine();
  60                 mothurOut("University of Michigan");
  61                 mothurOutEndLine();
  62                 mothurOut("pschloss@umich.edu");
  63                 mothurOutEndLine();
  64                 mothurOut("http://www.mothur.org");
  65                 mothurOutEndLine();
  66                 mothurOutEndLine();
  67                 mothurOut("When using, please cite:");
  68                 mothurOutEndLine();
  69                 mothurOut("Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.");
  70                 mothurOutEndLine();
  71                 mothurOutEndLine();
  72                 mothurOut("Distributed under the GNU General Public License");
  73                 mothurOutEndLine();
  74                 mothurOutEndLine();
  75                 mothurOut("Type 'help()' for information on the commands that are available");
  76                 mothurOutEndLine();
  77                 mothurOutEndLine();
  78                 mothurOut("Type 'quit()' to exit program");
  79                 mothurOutEndLine();
  80
  81
  82                 //srand(54321);
  83                 srand( (unsigned)time( NULL ) );
  84
  85                 Engine* mothur;
  86                 bool bail = 0;
  87                 string input;
  88
  89                 if(argc>1){
  90                         input = argv[1];
  91
  92                         if (input[0] == '#') {
  93                                 mothur = new ScriptEngine(argv[0], argv[1]);
  94                         }else{
  95                                 mothur = new BatchEngine(argv[0], argv[1]);
  96                         }
  97                 }
  98                 else{
  99                         mothur = new InteractEngine(argv[0]);
 100                 }
 101
 102                 while(bail == 0)                {       bail = mothur->getInput();                      }
 103
 104                 string outputDir = mothur->getOutputDir();
 105                 logFileName = outputDir + logFileName;
 106
 107                 delete mothur;
 108
 109 //              rename(log.c_str(), logFileName.c_str()); //logfile with timestamp
 110
 111                 return 0;
 112         }
 113         catch(exception& e) {
 114                 errorOut(e, "mothur", "main");
 115                 exit(1);
 116         }
 117 }
 118
 119 /**************************************************************************************************/
 120