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
  18 GlobalData* GlobalData::_uniqueInstance = 0;
  19 CommandFactory* CommandFactory::_uniqueInstance = 0;
  20 MothurOut* MothurOut::_uniqueInstance = 0;
  21
  22 /***********************************************************************/
  23 volatile int ctrlc_pressed = 0;
  24 void ctrlc_handler ( int sig ) {
  25         MothurOut* m = MothurOut::getInstance();
  26     ctrlc_pressed = 1;
  27         m->control_pressed = ctrlc_pressed;
  28
  29         if (m->executing) { //if mid command quit execution, else quit mothur
  30                 m->mothurOutEndLine(); m->mothurOut("quitting command...");  m->mothurOutEndLine();
  31         }else{
  32                 m->mothurOut("quitting mothur");  m->mothurOutEndLine();
  33                 exit(1);
  34         }
  35 }
  36 /***********************************************************************/
  37 int main(int argc, char *argv[]){
  38         MothurOut* m = MothurOut::getInstance();
  39         try {
  40
  41                 signal(SIGINT, ctrlc_handler );
  42
  43                 time_t ltime = time(NULL); /* calendar time */
  44                 string logFileName = "mothur." + toString(ltime) + ".logfile";
  45
  46                 #ifdef USE_MPI
  47                         MPI_Init(&argc, &argv);
  48                 #endif
  49
  50                 m->setFileName(logFileName);
  51
  52
  53                 //version
  54                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  55                         system("clear");
  56                         #if defined (__APPLE__) || (__MACH__)
  57                                 m->mothurOutJustToLog("Mac version");
  58                                 m->mothurOutEndLine(); m->mothurOutEndLine();
  59                         #else
  60                                 m->mothurOutJustToLog("Linux version");
  61                                 >m->mothurOutEndLine(); m->mothurOutEndLine();
  62                         #endif
  63
  64                 #else
  65                         system("CLS");
  66                         m->mothurOutJustToLog("Windows version");
  67                         m->mothurOutEndLine(); m->mothurOutEndLine();
  68                 #endif
  69
  70                 #ifdef USE_READLINE
  71                         m->mothurOutJustToLog("Using ReadLine");
  72                         m->mothurOutEndLine(); m->mothurOutEndLine();
  73                 #endif
  74
  75                 //header
  76                 m->mothurOut("mothur v.1.8");
  77                 m->mothurOutEndLine();
  78                 m->mothurOut("Last updated: 2/02/2010");
  79                 m->mothurOutEndLine();
  80                 m->mothurOutEndLine();
  81                 m->mothurOut("by");
  82                 m->mothurOutEndLine();
  83                 m->mothurOut("Patrick D. Schloss");
  84                 m->mothurOutEndLine();
  85                 m->mothurOutEndLine();
  86                 m->mothurOut("Department of Microbiology & Immunology");
  87                 m->mothurOutEndLine();
  88                 m->mothurOut("University of Michigan");
  89                 m->mothurOutEndLine();
  90                 m->mothurOut("pschloss@umich.edu");
  91                 m->mothurOutEndLine();
  92                 m->mothurOut("http://www.mothur.org");
  93                 m->mothurOutEndLine();
  94                 m->mothurOutEndLine();
  95                 m->mothurOut("When using, please cite:");
  96                 m->mothurOutEndLine();
  97                 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.");
  98                 m->mothurOutEndLine();
  99                 m->mothurOutEndLine();
 100                 m->mothurOut("Distributed under the GNU General Public License");
 101                 m->mothurOutEndLine();
 102                 m->mothurOutEndLine();
 103                 m->mothurOut("Type 'help()' for information on the commands that are available");
 104                 m->mothurOutEndLine();
 105                 m->mothurOutEndLine();
 106                 m->mothurOut("Type 'quit()' to exit program");
 107                 m->mothurOutEndLine();
 108
 109                 #ifdef USE_MPI
 110                         m->mothurOutJustToLog("Using MPI\n");
 111                 #endif
 112
 113                 //srand(54321);
 114                 srand( (unsigned)time( NULL ) );
 115
 116                 Engine* mothur;
 117                 bool bail = 0;
 118                 string input;
 119
 120                 if(argc>1){
 121                         input = argv[1];
 122
 123                         if (input[0] == '#') {
 124                                 m->mothurOutJustToLog("Script Mode");
 125                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 126
 127                                 mothur = new ScriptEngine(argv[0], argv[1]);
 128                         }else{
 129                                 m->mothurOutJustToLog("Batch Mode");
 130                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 131
 132                                 mothur = new BatchEngine(argv[0], argv[1]);
 133                         }
 134                 }
 135                 else{
 136                         m->mothurOutJustToLog("Interactive Mode");
 137                         m->mothurOutEndLine(); m->mothurOutEndLine();
 138
 139                         mothur = new InteractEngine(argv[0]);
 140                 }
 141
 142                 while(bail == 0)        {       bail = mothur->getInput();      }
 143
 144                 string outputDir = mothur->getOutputDir();
 145                 string newlogFileName = outputDir + logFileName;
 146
 147                 //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 148                 rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 149
 150                 delete mothur;
 151
 152                 #ifdef USE_MPI
 153                         MPI_Finalize();
 154                 #endif
 155
 156                 return 0;
 157         }
 158         catch(exception& e) {
 159                 m->errorOut(e, "mothur", "main");
 160                 exit(1);
 161         }
 162 }
 163
 164 /**************************************************************************************************/
 165