mothur.cpp

   1 /*\r
   2  *  interface.cpp\r
   3  *  \r
   4  *\r
   5  *  Created by Pat Schloss on 8/14/08.\r
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.\r
   7  *\r
   8  */\r
   9  \r
  10 #include "mothur.h"\r
  11 #include "engine.hpp"\r
  12 #include "globaldata.hpp"\r
  13 #include "mothurout.h"\r
  14 \r
  15 \r
  16 /**************************************************************************************************/\r
  17 \r
  18 GlobalData* GlobalData::_uniqueInstance = 0;\r
  19 CommandFactory* CommandFactory::_uniqueInstance = 0;\r
  20 MothurOut* MothurOut::_uniqueInstance = 0;\r
  21 \r
  22 /***********************************************************************/\r
  23 volatile int ctrlc_pressed = 0;\r
  24 void ctrlc_handler ( int sig ) {\r
  25         MothurOut* m = MothurOut::getInstance();\r
  26     ctrlc_pressed = 1;\r
  27         m->control_pressed = ctrlc_pressed;\r
  28         \r
  29         if (m->executing) { //if mid command quit execution, else quit mothur\r
  30                 m->mothurOutEndLine(); m->mothurOut("quitting command...");  m->mothurOutEndLine();\r
  31         }else{\r
  32                 m->mothurOut("quitting mothur");  m->mothurOutEndLine();\r
  33                 exit(1);\r
  34         }\r
  35 }\r
  36 /***********************************************************************/\r
  37 int main(int argc, char *argv[]){\r
  38         MothurOut* m = MothurOut::getInstance();\r
  39         try {\r
  40                 \r
  41                 signal(SIGINT, ctrlc_handler );\r
  42                                 \r
  43                 time_t ltime = time(NULL); /* calendar time */  \r
  44                 string logFileName = "mothur." + toString(ltime) + ".logfile";\r
  45                 \r
  46                 #ifdef USE_MPI\r
  47                         MPI_Init(&argc, &argv); \r
  48                 #endif\r
  49 \r
  50                 m->setFileName(logFileName);\r
  51                 \r
  52                                 \r
  53                 //version\r
  54                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
  55                         system("clear");\r
  56                         #if defined (__APPLE__) || (__MACH__)\r
  57                                 m->mothurOutJustToLog("Mac version");\r
  58                                 m->mothurOutEndLine(); m->mothurOutEndLine();\r
  59                         #else\r
  60                                 m->mothurOutJustToLog("Linux version");\r
  61                                 m->mothurOutEndLine(); m->mothurOutEndLine();\r
  62                         #endif\r
  63 \r
  64                 #else\r
  65                         system("CLS");\r
  66                         m->mothurOutJustToLog("Windows version");\r
  67                         m->mothurOutEndLine(); m->mothurOutEndLine();\r
  68                 #endif          \r
  69                 \r
  70                 #ifdef USE_READLINE\r
  71                         m->mothurOutJustToLog("Using ReadLine");\r
  72                         m->mothurOutEndLine(); m->mothurOutEndLine();\r
  73                 #endif\r
  74                 \r
  75                 #ifdef BIT_VERSION\r
  76                         m->mothurOutJustToLog("Running 64Bit Version");\r
  77                         m->mothurOutEndLine(); m->mothurOutEndLine();\r
  78                 #else\r
  79                         m->mothurOutJustToLog("Running 32Bit Version");\r
  80                         m->mothurOutEndLine(); m->mothurOutEndLine();\r
  81                 #endif\r
  82                 \r
  83                 //header\r
  84                 m->mothurOut("mothur v.1.11.0");\r
  85                 m->mothurOutEndLine();          \r
  86                 m->mothurOut("Last updated: 6/18/2010");\r
  87                 m->mothurOutEndLine();  \r
  88                 m->mothurOutEndLine();          \r
  89                 m->mothurOut("by");\r
  90                 m->mothurOutEndLine();          \r
  91                 m->mothurOut("Patrick D. Schloss");\r
  92                 m->mothurOutEndLine();\r
  93                 m->mothurOutEndLine();                  \r
  94                 m->mothurOut("Department of Microbiology & Immunology");\r
  95                 m->mothurOutEndLine();  \r
  96                 m->mothurOut("University of Michigan");\r
  97                 m->mothurOutEndLine();                  \r
  98                 m->mothurOut("pschloss@umich.edu");\r
  99                 m->mothurOutEndLine();          \r
 100                 m->mothurOut("http://www.mothur.org");\r
 101                 m->mothurOutEndLine();\r
 102                 m->mothurOutEndLine();\r
 103                 m->mothurOut("When using, please cite:");\r
 104                 m->mothurOutEndLine();\r
 105                 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.");\r
 106                 m->mothurOutEndLine();  \r
 107                 m->mothurOutEndLine();          \r
 108                 m->mothurOut("Distributed under the GNU General Public License");\r
 109                 m->mothurOutEndLine();\r
 110                 m->mothurOutEndLine();                  \r
 111                 m->mothurOut("Type 'help()' for information on the commands that are available");\r
 112                 m->mothurOutEndLine();\r
 113                 m->mothurOutEndLine();                  \r
 114                 m->mothurOut("Type 'quit()' to exit program");\r
 115                 m->mothurOutEndLine();  \r
 116                 \r
 117                 #ifdef USE_MPI\r
 118                         m->mothurOutJustToLog("Using MPI\tversion ");\r
 119                         int version, subversion;\r
 120                         MPI_Get_version(&version, &subversion);\r
 121                         m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");\r
 122                 #endif\r
 123                 \r
 124                 //srand(54321);\r
 125                 srand( (unsigned)time( NULL ) );\r
 126                 \r
 127                 Engine* mothur;\r
 128                 bool bail = 0;\r
 129                 string input;\r
 130 \r
 131                 if(argc>1){\r
 132                         input = argv[1];\r
 133 \r
 134                         if (input[0] == '#') {\r
 135                                 m->mothurOutJustToLog("Script Mode");\r
 136                                 m->mothurOutEndLine(); m->mothurOutEndLine();\r
 137 \r
 138                                 mothur = new ScriptEngine(argv[0], argv[1]);\r
 139                         }else{\r
 140                                 m->mothurOutJustToLog("Batch Mode");\r
 141                                 m->mothurOutEndLine(); m->mothurOutEndLine();\r
 142                                 \r
 143                                 mothur = new BatchEngine(argv[0], argv[1]);\r
 144                         }\r
 145                 }\r
 146                 else{\r
 147                         m->mothurOutJustToLog("Interactive Mode");\r
 148                         m->mothurOutEndLine(); m->mothurOutEndLine();\r
 149                         \r
 150                         mothur = new InteractEngine(argv[0]);   \r
 151                 }\r
 152                 \r
 153                 while(bail == 0)        {       bail = mothur->getInput();      }\r
 154                 \r
 155                 //closes logfile so we can rename\r
 156                 m->closeLog();\r
 157                 \r
 158                 string outputDir = mothur->getOutputDir();\r
 159                 string tempLog = mothur->getLogFileName();\r
 160                 bool append = mothur->getAppend();\r
 161                 \r
 162                 string newlogFileName;\r
 163                 if (tempLog != "") {\r
 164                         newlogFileName = outputDir + tempLog;\r
 165                         \r
 166                         if (!append) {  \r
 167                                 //need this because m->mothurOut makes the logfile, but doesn't know where to put it\r
 168                                 rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp\r
 169 \r
 170                         }else {\r
 171                                 ofstream outNewLog;\r
 172                                 openOutputFileAppend(newlogFileName, outNewLog);\r
 173                                 outNewLog << endl << endl << "*********************************************************************************" << endl << endl;\r
 174                                 outNewLog.close();\r
 175                                 \r
 176                                 appendFiles(logFileName, newlogFileName);\r
 177                                 remove(logFileName.c_str());\r
 178                         }\r
 179                 }else{  \r
 180                         newlogFileName = outputDir + logFileName;\r
 181                         //need this because m->mothurOut makes the logfile, but doesn't know where to put it\r
 182                         rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp\r
 183                 }\r
 184                 \r
 185                                 \r
 186                 delete mothur;\r
 187                 \r
 188                 #ifdef USE_MPI\r
 189                         MPI_Finalize();\r
 190                 #endif\r
 191                 \r
 192                 return 0;\r
 193         }\r
 194         catch(exception& e) {\r
 195                 m->errorOut(e, "mothur", "main");\r
 196                 exit(1);\r
 197         }\r
 198 }\r
 199 \r
 200 /**************************************************************************************************/\r
 201 \r