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