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 #include "mothurout.h"
  14
  15 /**************************************************************************************************/
  16
  17 GlobalData* GlobalData::_uniqueInstance = 0;
  18 CommandFactory* CommandFactory::_uniqueInstance = 0;
  19 MothurOut* MothurOut::_uniqueInstance = 0;
  20
  21 int main(int argc, char *argv[]){
  22         MothurOut* m = MothurOut::getInstance();
  23         try {
  24
  25                 //string log = "mothur.logFile";
  26                 //remove(log.c_str());
  27
  28                 time_t ltime = time(NULL); /* calendar time */
  29                 string logFileName = "mothur." + toString(ltime) + ".logfile";
  30
  31                 m->setFileName(logFileName);
  32
  33                 //version
  34                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  35                         system("clear");
  36                         #if defined (__APPLE__) || (__MACH__)
  37                                 m->mothurOutJustToLog("Mac version");
  38                                 m->mothurOutEndLine(); m->mothurOutEndLine();
  39                         #else
  40                                 m->mothurOutJustToLog("Linux version");
  41                                 >m->mothurOutEndLine(); m->mothurOutEndLine();
  42                         #endif
  43
  44                 #else
  45                         system("CLS");
  46                         m->mothurOutJustToLog("Windows version");
  47                         m->mothurOutEndLine(); m->mothurOutEndLine();
  48                 #endif
  49
  50                 #ifdef USE_READLINE
  51                         m->mothurOutJustToLog("Using ReadLine");
  52                         m->mothurOutEndLine(); m->mothurOutEndLine();
  53                 #endif
  54
  55                 //header
  56                 m->mothurOut("mothur v.1.8");
  57                 m->mothurOutEndLine();
  58                 m->mothurOut("Last updated: 2/02/2010");
  59                 m->mothurOutEndLine();
  60                 m->mothurOutEndLine();
  61                 m->mothurOut("by");
  62                 m->mothurOutEndLine();
  63                 m->mothurOut("Patrick D. Schloss");
  64                 m->mothurOutEndLine();
  65                 m->mothurOutEndLine();
  66                 m->mothurOut("Department of Microbiology & Immunology");
  67                 m->mothurOutEndLine();
  68                 m->mothurOut("University of Michigan");
  69                 m->mothurOutEndLine();
  70                 m->mothurOut("pschloss@umich.edu");
  71                 m->mothurOutEndLine();
  72                 m->mothurOut("http://www.mothur.org");
  73                 m->mothurOutEndLine();
  74                 m->mothurOutEndLine();
  75                 m->mothurOut("When using, please cite:");
  76                 m->mothurOutEndLine();
  77                 m->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.");
  78                 m->mothurOutEndLine();
  79                 m->mothurOutEndLine();
  80                 m->mothurOut("Distributed under the GNU General Public License");
  81                 m->mothurOutEndLine();
  82                 m->mothurOutEndLine();
  83                 m->mothurOut("Type 'help()' for information on the commands that are available");
  84                 m->mothurOutEndLine();
  85                 m->mothurOutEndLine();
  86                 m->mothurOut("Type 'quit()' to exit program");
  87                 m->mothurOutEndLine();
  88
  89
  90                 //srand(54321);
  91                 srand( (unsigned)time( NULL ) );
  92
  93                 Engine* mothur;
  94                 bool bail = 0;
  95                 string input;
  96
  97                 if(argc>1){
  98                         input = argv[1];
  99
 100                         if (input[0] == '#') {
 101                                 m->mothurOutJustToLog("Script Mode");
 102                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 103
 104                                 mothur = new ScriptEngine(argv[0], argv[1]);
 105                         }else{
 106                                 m->mothurOutJustToLog("Batch Mode");
 107                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 108
 109                                 mothur = new BatchEngine(argv[0], argv[1]);
 110                         }
 111                 }
 112                 else{
 113                         m->mothurOutJustToLog("Interactive Mode");
 114                         m->mothurOutEndLine(); m->mothurOutEndLine();
 115
 116                         mothur = new InteractEngine(argv[0]);
 117                 }
 118
 119                 while(bail == 0)                {       bail = mothur->getInput();                      }
 120
 121                 string outputDir = mothur->getOutputDir();
 122                 string newlogFileName = outputDir + logFileName;
 123
 124                 //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 125                 rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 126
 127                 delete mothur;
 128
 129                 return 0;
 130         }
 131         catch(exception& e) {
 132                 m->errorOut(e, "mothur", "main");
 133                 exit(1);
 134         }
 135 }
 136
 137 /**************************************************************************************************/
 138