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 /***********************************************************************/
  22 volatile int ctrlc_pressed = 0;
  23 void ctrlc_handler ( int sig ) {
  24         MothurOut* m = MothurOut::getInstance();
  25     ctrlc_pressed = 1;
  26         m->control_pressed = ctrlc_pressed;
  27 }
  28 /***********************************************************************/
  29 int main(int argc, char *argv[]){
  30         MothurOut* m = MothurOut::getInstance();
  31         try {
  32
  33                 signal(SIGINT, ctrlc_handler );
  34
  35                 time_t ltime = time(NULL); /* calendar time */
  36                 string logFileName = "mothur." + toString(ltime) + ".logfile";
  37
  38                 m->setFileName(logFileName);
  39
  40                 //version
  41                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  42                         system("clear");
  43                         #if defined (__APPLE__) || (__MACH__)
  44                                 m->mothurOutJustToLog("Mac version");
  45                                 m->mothurOutEndLine(); m->mothurOutEndLine();
  46                         #else
  47                                 m->mothurOutJustToLog("Linux version");
  48                                 >m->mothurOutEndLine(); m->mothurOutEndLine();
  49                         #endif
  50
  51                 #else
  52                         system("CLS");
  53                         m->mothurOutJustToLog("Windows version");
  54                         m->mothurOutEndLine(); m->mothurOutEndLine();
  55                 #endif
  56
  57                 #ifdef USE_READLINE
  58                         m->mothurOutJustToLog("Using ReadLine");
  59                         m->mothurOutEndLine(); m->mothurOutEndLine();
  60                 #endif
  61
  62                 //header
  63                 m->mothurOut("mothur v.1.8");
  64                 m->mothurOutEndLine();
  65                 m->mothurOut("Last updated: 2/02/2010");
  66                 m->mothurOutEndLine();
  67                 m->mothurOutEndLine();
  68                 m->mothurOut("by");
  69                 m->mothurOutEndLine();
  70                 m->mothurOut("Patrick D. Schloss");
  71                 m->mothurOutEndLine();
  72                 m->mothurOutEndLine();
  73                 m->mothurOut("Department of Microbiology & Immunology");
  74                 m->mothurOutEndLine();
  75                 m->mothurOut("University of Michigan");
  76                 m->mothurOutEndLine();
  77                 m->mothurOut("pschloss@umich.edu");
  78                 m->mothurOutEndLine();
  79                 m->mothurOut("http://www.mothur.org");
  80                 m->mothurOutEndLine();
  81                 m->mothurOutEndLine();
  82                 m->mothurOut("When using, please cite:");
  83                 m->mothurOutEndLine();
  84                 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.");
  85                 m->mothurOutEndLine();
  86                 m->mothurOutEndLine();
  87                 m->mothurOut("Distributed under the GNU General Public License");
  88                 m->mothurOutEndLine();
  89                 m->mothurOutEndLine();
  90                 m->mothurOut("Type 'help()' for information on the commands that are available");
  91                 m->mothurOutEndLine();
  92                 m->mothurOutEndLine();
  93                 m->mothurOut("Type 'quit()' to exit program");
  94                 m->mothurOutEndLine();
  95
  96
  97                 //srand(54321);
  98                 srand( (unsigned)time( NULL ) );
  99
 100                 Engine* mothur;
 101                 bool bail = 0;
 102                 string input;
 103
 104                 if(argc>1){
 105                         input = argv[1];
 106
 107                         if (input[0] == '#') {
 108                                 m->mothurOutJustToLog("Script Mode");
 109                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 110
 111                                 mothur = new ScriptEngine(argv[0], argv[1]);
 112                         }else{
 113                                 m->mothurOutJustToLog("Batch Mode");
 114                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 115
 116                                 mothur = new BatchEngine(argv[0], argv[1]);
 117                         }
 118                 }
 119                 else{
 120                         m->mothurOutJustToLog("Interactive Mode");
 121                         m->mothurOutEndLine(); m->mothurOutEndLine();
 122
 123                         mothur = new InteractEngine(argv[0]);
 124                 }
 125
 126                 while(bail == 0)                {       bail = mothur->getInput();                      }
 127
 128                 string outputDir = mothur->getOutputDir();
 129                 string newlogFileName = outputDir + logFileName;
 130
 131                 //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 132                 rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 133
 134                 delete mothur;
 135
 136                 return 0;
 137         }
 138         catch(exception& e) {
 139                 m->errorOut(e, "mothur", "main");
 140                 exit(1);
 141         }
 142 }
 143
 144 /**************************************************************************************************/
 145