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 logFileName = "mothur.logFile";
  24                 remove(logFileName.c_str());
  25
  26                 //version
  27                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  28                         system("clear");
  29                         #if defined (__APPLE__) || (__MACH__)
  30                                 mothurOutJustToLog("Mac version");
  31                                 mothurOutEndLine(); mothurOutEndLine();
  32                         #else
  33                                 mothurOutJustToLog("Linux version");
  34                                 mothurOutEndLine(); mothurOutEndLine();
  35                         #endif
  36
  37                 #else
  38                         system("CLS");
  39                         mothurOutJustToLog("Windows version");
  40                         mothurOutEndLine(); mothurOutEndLine();
  41                 #endif
  42
  43
  44                 //header
  45                 mothurOut("mothur v.1.7.2");
  46                 mothurOutEndLine();
  47                 mothurOut("Last updated: 12/04/2009");
  48                 mothurOutEndLine();
  49                 mothurOutEndLine();
  50                 mothurOut("by");
  51                 mothurOutEndLine();
  52                 mothurOut("Patrick D. Schloss");
  53                 mothurOutEndLine();
  54                 mothurOutEndLine();
  55                 mothurOut("Department of Microbiology & Immunology");
  56                 mothurOutEndLine();
  57                 mothurOut("University of Michigan");
  58                 mothurOutEndLine();
  59                 mothurOut("pschloss@umich.edu");
  60                 mothurOutEndLine();
  61                 mothurOut("http://www.mothur.org");
  62                 mothurOutEndLine();
  63                 mothurOutEndLine();
  64                 mothurOut("When using, please cite:");
  65                 mothurOutEndLine();
  66                 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.");
  67                 mothurOutEndLine();
  68                 mothurOutEndLine();
  69                 mothurOut("Distributed under the GNU General Public License");
  70                 mothurOutEndLine();
  71                 mothurOutEndLine();
  72                 mothurOut("Type 'help()' for information on the commands that are available");
  73                 mothurOutEndLine();
  74                 mothurOutEndLine();
  75                 mothurOut("Type 'quit()' to exit program");
  76                 mothurOutEndLine();
  77
  78
  79                 //srand(54321);
  80                 srand( (unsigned)time( NULL ) );
  81
  82                 Engine* mothur;
  83                 bool bail = 0;
  84                 string input;
  85
  86                 if(argc>1){
  87                         input = argv[1];
  88
  89                         if (input[0] == '#') {
  90                                 mothur = new ScriptEngine(argv[0], argv[1]);
  91                         }else{
  92                                 mothur = new BatchEngine(argv[0], argv[1]);
  93                         }
  94                 }
  95                 else{
  96                         mothur = new InteractEngine(argv[0]);
  97                 }
  98
  99                 //used to intercept the terminate signal, so instead of terminating mothur it will end a command
 100                 //void (*prev_fn)(int);
 101                 //prev_fn = signal(SIGTERM, mothur->terminateCommand(0));
 102
 103                 //if (prev_fn==SIG_IGN) signal (SIGTERM,SIG_IGN);
 104
 105
 106                 while(bail == 0)                {       bail = mothur->getInput();                      }
 107
 108                 delete mothur;
 109
 110                 return 0;
 111         }
 112         catch(exception& e) {
 113                 errorOut(e, "mothur", "main");
 114                 exit(1);
 115         }
 116 }
 117
 118 /**************************************************************************************************/
 119