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                 #ifdef USE_MPI
  46                         MPI_Init(&argc, &argv);
  47                 #endif
  48
  49                 m->setFileName(logFileName);
  50
  51
  52                 //version
  53                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  54                         system("clear");
  55                         #if defined (__APPLE__) || (__MACH__)
  56                                 m->mothurOutJustToLog("Mac version");
  57                                 m->mothurOutEndLine(); m->mothurOutEndLine();
  58                         #else
  59                                 m->mothurOutJustToLog("Linux version");
  60                                 m->mothurOutEndLine(); m->mothurOutEndLine();
  61                         #endif
  62
  63                 #else
  64                         system("CLS");
  65                         m->mothurOutJustToLog("Windows version");
  66                         m->mothurOutEndLine(); m->mothurOutEndLine();
  67                 #endif
  68
  69                 #ifdef USE_READLINE
  70                         m->mothurOutJustToLog("Using ReadLine");
  71                         m->mothurOutEndLine(); m->mothurOutEndLine();
  72                 #endif
  73
  74                 #ifdef MOTHUR_FILES
  75                         string temp = MOTHUR_FILES;
  76                         m->setDefaultPath(temp);
  77                         m->mothurOutJustToLog("Using default file location " + temp);
  78                         m->mothurOutEndLine(); m->mothurOutEndLine();
  79                 #endif
  80
  81                 #ifdef BIT_VERSION
  82                         m->mothurOutJustToLog("Running 64Bit Version");
  83                         m->mothurOutEndLine(); m->mothurOutEndLine();
  84                 #else
  85                         m->mothurOutJustToLog("Running 32Bit Version");
  86                         m->mothurOutEndLine(); m->mothurOutEndLine();
  87                 #endif
  88
  89                 //header
  90                 m->mothurOut("mothur v.1.11.0");
  91                 m->mothurOutEndLine();
  92                 m->mothurOut("Last updated: 6/18/2010");
  93                 m->mothurOutEndLine();
  94                 m->mothurOutEndLine();
  95                 m->mothurOut("by");
  96                 m->mothurOutEndLine();
  97                 m->mothurOut("Patrick D. Schloss");
  98                 m->mothurOutEndLine();
  99                 m->mothurOutEndLine();
 100                 m->mothurOut("Department of Microbiology & Immunology");
 101                 m->mothurOutEndLine();
 102                 m->mothurOut("University of Michigan");
 103                 m->mothurOutEndLine();
 104                 m->mothurOut("pschloss@umich.edu");
 105                 m->mothurOutEndLine();
 106                 m->mothurOut("http://www.mothur.org");
 107                 m->mothurOutEndLine();
 108                 m->mothurOutEndLine();
 109                 m->mothurOut("When using, please cite:");
 110                 m->mothurOutEndLine();
 111                 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.");
 112                 m->mothurOutEndLine();
 113                 m->mothurOutEndLine();
 114                 m->mothurOut("Distributed under the GNU General Public License");
 115                 m->mothurOutEndLine();
 116                 m->mothurOutEndLine();
 117                 m->mothurOut("Type 'help()' for information on the commands that are available");
 118                 m->mothurOutEndLine();
 119                 m->mothurOutEndLine();
 120                 m->mothurOut("Type 'quit()' to exit program");
 121                 m->mothurOutEndLine();
 122
 123                 #ifdef USE_MPI
 124                         m->mothurOutJustToLog("Using MPI\tversion ");
 125                         int version, subversion;
 126                         MPI_Get_version(&version, &subversion);
 127                         m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
 128                 #endif
 129
 130                 //srand(54321);
 131                 srand( (unsigned)time( NULL ) );
 132
 133                 Engine* mothur;
 134                 bool bail = 0;
 135                 string input;
 136
 137                 if(argc>1){
 138                         input = argv[1];
 139
 140                         if (input[0] == '#') {
 141                                 m->mothurOutJustToLog("Script Mode");
 142                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 143
 144                                 mothur = new ScriptEngine(argv[0], argv[1]);
 145                         }else{
 146                                 m->mothurOutJustToLog("Batch Mode");
 147                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 148
 149                                 mothur = new BatchEngine(argv[0], argv[1]);
 150                         }
 151                 }
 152                 else{
 153                         m->mothurOutJustToLog("Interactive Mode");
 154                         m->mothurOutEndLine(); m->mothurOutEndLine();
 155
 156                         mothur = new InteractEngine(argv[0]);
 157                 }
 158
 159                 while(bail == 0)        {       bail = mothur->getInput();      }
 160
 161                 //closes logfile so we can rename
 162                 m->closeLog();
 163
 164                 string outputDir = mothur->getOutputDir();
 165                 string tempLog = mothur->getLogFileName();
 166                 bool append = mothur->getAppend();
 167
 168                 string newlogFileName;
 169                 if (tempLog != "") {
 170                         newlogFileName = outputDir + tempLog;
 171
 172                         if (!append) {
 173                                 //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 174                                 rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 175
 176                         }else {
 177                                 ofstream outNewLog;
 178                                 openOutputFileAppend(newlogFileName, outNewLog);
 179                                 outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
 180                                 outNewLog.close();
 181
 182                                 appendFiles(logFileName, newlogFileName);
 183                                 remove(logFileName.c_str());
 184                         }
 185                 }else{
 186                         newlogFileName = outputDir + logFileName;
 187                         //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 188                         rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 189                 }
 190
 191
 192                 delete mothur;
 193
 194                 #ifdef USE_MPI
 195                         MPI_Finalize();
 196                 #endif
 197
 198                 return 0;
 199         }
 200         catch(exception& e) {
 201                 m->errorOut(e, "mothur", "main");
 202                 exit(1);
 203         }
 204 }
 205
 206 /**************************************************************************************************/
 207