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 CommandFactory* CommandFactory::_uniqueInstance = 0;
  18 MothurOut* MothurOut::_uniqueInstance = 0;
  19
  20 /***********************************************************************/
  21 volatile int ctrlc_pressed = 0;
  22 void ctrlc_handler ( int sig ) {
  23         MothurOut* m = MothurOut::getInstance();
  24     ctrlc_pressed = 1;
  25         m->control_pressed = ctrlc_pressed;
  26
  27         if (m->executing) { //if mid command quit execution, else quit mothur
  28                 m->mothurOutEndLine(); m->mothurOut("quitting command...");  m->mothurOutEndLine();
  29         }else{
  30                 m->mothurOut("quitting mothur");  m->mothurOutEndLine();
  31                 exit(1);
  32         }
  33 }
  34 /***********************************************************************/
  35 int main(int argc, char *argv[]){
  36         MothurOut* m = MothurOut::getInstance();
  37         try {
  38                 signal(SIGINT, ctrlc_handler );
  39
  40                 time_t ltime = time(NULL); /* calendar time */
  41                 string logFileName = "mothur." + toString(ltime) + ".logfile";
  42
  43                 #ifdef USE_MPI
  44                         MPI_Init(&argc, &argv);
  45                 #endif
  46
  47                 m->setFileName(logFileName);
  48
  49
  50                 //version
  51                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  52                         system("clear");
  53                         #if defined (__APPLE__) || (__MACH__)
  54                                 m->mothurOutJustToLog("Mac version");
  55                                 m->mothurOutEndLine(); m->mothurOutEndLine();
  56                         #else
  57                                 m->mothurOutJustToLog("Linux version");
  58                                 m->mothurOutEndLine(); m->mothurOutEndLine();
  59                         #endif
  60
  61                 #else
  62                         system("CLS");
  63                         m->mothurOutJustToLog("Windows version");
  64                         m->mothurOutEndLine(); m->mothurOutEndLine();
  65                 #endif
  66
  67                 #ifdef USE_READLINE
  68                         m->mothurOutJustToLog("Using ReadLine");
  69                         m->mothurOutEndLine(); m->mothurOutEndLine();
  70                 #endif
  71
  72                 #ifdef MOTHUR_FILES
  73                         string temp = MOTHUR_FILES;
  74
  75                         //add / to name if needed
  76                         string lastChar = temp.substr(temp.length()-1);
  77                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  78                                 if (lastChar != "/") { temp += "/"; }
  79                         #else
  80                                 if (lastChar != "\\") { temp += "\\"; }
  81                         #endif
  82
  83                         temp = m->getFullPathName(temp);
  84                         m->setDefaultPath(temp);
  85
  86                         m->mothurOutJustToLog("Using default file location " + temp);
  87                         m->mothurOutEndLine(); m->mothurOutEndLine();
  88                 #endif
  89
  90                 #ifdef BIT_VERSION
  91                         m->mothurOutJustToLog("Running 64Bit Version");
  92                         m->mothurOutEndLine(); m->mothurOutEndLine();
  93                 #else
  94                         m->mothurOutJustToLog("Running 32Bit Version");
  95                         m->mothurOutEndLine(); m->mothurOutEndLine();
  96                 #endif
  97
  98                 //get releaseDate from Make
  99                 string releaseDate = RELEASE_DATE;
 100                 string mothurVersion = VERSION;
 101                 m->setReleaseDate(releaseDate);
 102                 m->setVersion(mothurVersion);
 103
 104                 //header
 105                 m->mothurOut("mothur v." + mothurVersion);
 106                 m->mothurOutEndLine();
 107                 m->mothurOut("Last updated: " + releaseDate);
 108                 m->mothurOutEndLine();
 109                 m->mothurOutEndLine();
 110                 m->mothurOut("by");
 111                 m->mothurOutEndLine();
 112                 m->mothurOut("Patrick D. Schloss");
 113                 m->mothurOutEndLine();
 114                 m->mothurOutEndLine();
 115                 m->mothurOut("Department of Microbiology & Immunology");
 116                 m->mothurOutEndLine();
 117                 m->mothurOut("University of Michigan");
 118                 m->mothurOutEndLine();
 119                 m->mothurOut("pschloss@umich.edu");
 120                 m->mothurOutEndLine();
 121                 m->mothurOut("http://www.mothur.org");
 122                 m->mothurOutEndLine();
 123                 m->mothurOutEndLine();
 124                 m->mothurOut("When using, please cite:");
 125                 m->mothurOutEndLine();
 126                 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.");
 127                 m->mothurOutEndLine();
 128                 m->mothurOutEndLine();
 129                 m->mothurOut("Distributed under the GNU General Public License");
 130                 m->mothurOutEndLine();
 131                 m->mothurOutEndLine();
 132                 m->mothurOut("Type 'help()' for information on the commands that are available");
 133                 m->mothurOutEndLine();
 134                 m->mothurOutEndLine();
 135                 m->mothurOut("Type 'quit()' to exit program");
 136                 m->mothurOutEndLine();
 137
 138                 #ifdef USE_MPI
 139                         m->mothurOutJustToLog("Using MPI\tversion ");
 140                         int version, subversion;
 141                         MPI_Get_version(&version, &subversion);
 142                         m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
 143                 #endif
 144
 145                 //srand(54321);
 146                 srand( (unsigned)time( NULL ) );
 147
 148                 Engine* mothur;
 149                 bool bail = 0;
 150                 string input;
 151
 152                 if(argc>1){
 153                         input = argv[1];
 154
 155                         if (input[0] == '#') {
 156                                 m->mothurOutJustToLog("Script Mode");
 157                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 158
 159                                 mothur = new ScriptEngine(argv[0], argv[1]);
 160                         }else{
 161                                 m->mothurOutJustToLog("Batch Mode");
 162                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 163
 164                                 mothur = new BatchEngine(argv[0], argv[1]);
 165                         }
 166                 }
 167                 else{
 168                         m->mothurOutJustToLog("Interactive Mode");
 169                         m->mothurOutEndLine(); m->mothurOutEndLine();
 170
 171                         mothur = new InteractEngine(argv[0]);
 172                 }
 173
 174                 while(bail == 0)        {       bail = mothur->getInput();      }
 175
 176                 //closes logfile so we can rename
 177                 m->closeLog();
 178
 179                 string outputDir = mothur->getOutputDir();
 180                 string tempLog = mothur->getLogFileName();
 181                 bool append = mothur->getAppend();
 182
 183                 string newlogFileName;
 184                 if (tempLog != "") {
 185                         newlogFileName = outputDir + tempLog;
 186
 187                         if (!append) {
 188                                 //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 189                                 rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 190
 191                         }else {
 192                                 ofstream outNewLog;
 193                                 m->openOutputFileAppend(newlogFileName, outNewLog);
 194                                 outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
 195                                 outNewLog.close();
 196
 197                                 m->appendFiles(logFileName, newlogFileName);
 198                                 remove(logFileName.c_str());
 199                         }
 200                 }else{
 201                         newlogFileName = outputDir + logFileName;
 202                         //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 203                         rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 204                 }
 205
 206
 207                 delete mothur;
 208
 209                 #ifdef USE_MPI
 210                         MPI_Finalize();
 211                 #endif
 212
 213                 return 0;
 214         }
 215         catch(exception& e) {
 216                 m->errorOut(e, "mothur", "main");
 217                 exit(1);
 218         }
 219 }
 220
 221 /**************************************************************************************************/
 222