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