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                 string log = "mothur.logFile";
  23                 remove(log.c_str());
  24
  25                 time_t ltime = time(NULL); /* calendar time */
  26                 string logFileName = "mothur." + toString(ltime) + ".logfile";
  27
  28                 //version
  29                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  30                         system("clear");
  31                         #if defined (__APPLE__) || (__MACH__)
  32                                 mothurOutJustToLog("Mac version");
  33                                 mothurOutEndLine(); mothurOutEndLine();
  34                         #else
  35                                 mothurOutJustToLog("Linux version");
  36                                 mothurOutEndLine(); mothurOutEndLine();
  37                         #endif
  38
  39                 #else
  40                         system("CLS");
  41                         mothurOutJustToLog("Windows version");
  42                         mothurOutEndLine(); mothurOutEndLine();
  43                 #endif
  44
  45                 #ifdef USE_READLINE
  46                         mothurOutJustToLog("Using ReadLine");
  47                         mothurOutEndLine(); mothurOutEndLine();
  48                 #endif
  49
  50                 //header
  51                 mothurOut("mothur v.1.8");
  52                 mothurOutEndLine();
  53                 mothurOut("Last updated: 2/02/2010");
  54                 mothurOutEndLine();
  55                 mothurOutEndLine();
  56                 mothurOut("by");
  57                 mothurOutEndLine();
  58                 mothurOut("Patrick D. Schloss");
  59                 mothurOutEndLine();
  60                 mothurOutEndLine();
  61                 mothurOut("Department of Microbiology & Immunology");
  62                 mothurOutEndLine();
  63                 mothurOut("University of Michigan");
  64                 mothurOutEndLine();
  65                 mothurOut("pschloss@umich.edu");
  66                 mothurOutEndLine();
  67                 mothurOut("http://www.mothur.org");
  68                 mothurOutEndLine();
  69                 mothurOutEndLine();
  70                 mothurOut("When using, please cite:");
  71                 mothurOutEndLine();
  72                 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.");
  73                 mothurOutEndLine();
  74                 mothurOutEndLine();
  75                 mothurOut("Distributed under the GNU General Public License");
  76                 mothurOutEndLine();
  77                 mothurOutEndLine();
  78                 mothurOut("Type 'help()' for information on the commands that are available");
  79                 mothurOutEndLine();
  80                 mothurOutEndLine();
  81                 mothurOut("Type 'quit()' to exit program");
  82                 mothurOutEndLine();
  83
  84
  85                 //srand(54321);
  86                 srand( (unsigned)time( NULL ) );
  87
  88                 Engine* mothur;
  89                 bool bail = 0;
  90                 string input;
  91
  92                 if(argc>1){
  93                         input = argv[1];
  94
  95                         if (input[0] == '#') {
  96                                 mothurOutJustToLog("Script Mode");
  97                                 mothurOutEndLine(); mothurOutEndLine();
  98
  99                                 mothur = new ScriptEngine(argv[0], argv[1]);
 100                         }else{
 101                                 mothurOutJustToLog("Batch Mode");
 102                                 mothurOutEndLine(); mothurOutEndLine();
 103
 104                                 mothur = new BatchEngine(argv[0], argv[1]);
 105                         }
 106                 }
 107                 else{
 108                         mothurOutJustToLog("Interactive Mode");
 109                         mothurOutEndLine(); mothurOutEndLine();
 110
 111                         mothur = new InteractEngine(argv[0]);
 112                 }
 113
 114                 while(bail == 0)                {       bail = mothur->getInput();                      }
 115
 116                 string outputDir = mothur->getOutputDir();
 117                 logFileName = outputDir + logFileName;
 118
 119                 //need this because mothur.h makes the logfile, but doesn't know where to put it
 120                 rename(log.c_str(), logFileName.c_str()); //logfile with timestamp
 121
 122                 delete mothur;
 123
 124                 return 0;
 125         }
 126         catch(exception& e) {
 127                 errorOut(e, "mothur", "main");
 128                 exit(1);
 129         }
 130 }
 131
 132 /**************************************************************************************************/
 133