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
  18 int main(int argc, char *argv[]){
  19         try {
  20
  21                 //remove old logfile
  22                 string logFileName = "mothur.logFile";
  23                 remove(logFileName.c_str());
  24
  25                 //version
  26                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  27                         system("clear");
  28                         #if defined (__APPLE__) || (__MACH__)
  29                                 mothurOutJustToLog("Mac version");
  30                                 mothurOutEndLine(); mothurOutEndLine();
  31                         #else
  32                                 mothurOutJustToLog("Linux version");
  33                                 mothurOutEndLine(); mothurOutEndLine();
  34                         #endif
  35
  36                 #else
  37                         system("CLS");
  38                         mothurOutJustToLog("Windows version");
  39                         mothurOutEndLine(); mothurOutEndLine();
  40                 #endif
  41
  42
  43                 //header
  44                 mothurOut("mothur v.1.7.2");
  45                 mothurOutEndLine();
  46                 mothurOut("Last updated: 12/04/2009");
  47                 mothurOutEndLine();
  48                 mothurOutEndLine();
  49                 mothurOut("by");
  50                 mothurOutEndLine();
  51                 mothurOut("Patrick D. Schloss");
  52                 mothurOutEndLine();
  53                 mothurOutEndLine();
  54                 mothurOut("Department of Microbiology & Immunology");
  55                 mothurOutEndLine();
  56                 mothurOut("University of Michigan");
  57                 mothurOutEndLine();
  58                 mothurOut("pschloss@umich.edu");
  59                 mothurOutEndLine();
  60                 mothurOut("http://www.mothur.org");
  61                 mothurOutEndLine();
  62                 mothurOutEndLine();
  63                 mothurOut("When using, please cite:");
  64                 mothurOutEndLine();
  65                 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.");
  66                 mothurOutEndLine();
  67                 mothurOutEndLine();
  68                 mothurOut("Distributed under the GNU General Public License");
  69                 mothurOutEndLine();
  70                 mothurOutEndLine();
  71                 mothurOut("Type 'help()' for information on the commands that are available");
  72                 mothurOutEndLine();
  73                 mothurOutEndLine();
  74                 mothurOut("Type 'quit()' to exit program");
  75                 mothurOutEndLine();
  76
  77
  78                 //srand(54321);
  79                 srand( (unsigned)time( NULL ) );
  80
  81                 Engine* mothur;
  82                 bool bail = 0;
  83                 string input;
  84
  85                 if(argc>1){
  86                         input = argv[1];
  87
  88                         if (input[0] == '#') {
  89                                 mothur = new ScriptEngine(argv[0], argv[1]);
  90                         }else{
  91                                 mothur = new BatchEngine(argv[0], argv[1]);
  92                         }
  93                 }
  94                 else{
  95                         mothur = new InteractEngine(argv[0]);
  96                 }
  97
  98                 //used to intercept the terminate signal, so instead of terminating mothur it will end a command
  99                 //void (*prev_fn)(int);
 100                 //prev_fn = signal(SIGTERM, mothur->terminateCommand(0));
 101
 102                 //if (prev_fn==SIG_IGN) signal (SIGTERM,SIG_IGN);
 103
 104
 105                 while(bail == 0)                {       bail = mothur->getInput();                      }
 106
 107                 delete mothur;
 108
 109                 return 0;
 110         }
 111         catch(exception& e) {
 112                 errorOut(e, "mothur", "main");
 113                 exit(1);
 114         }
 115 }
 116
 117 /**************************************************************************************************/
 118