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                 signal(SIGINT, ctrlc_handler );
  40
  41                 time_t ltime = time(NULL); /* calendar time */
  42                 string logFileName = "mothur." + toString(ltime) + ".logfile";
  43
  44                 #ifdef USE_MPI
  45                         MPI_Init(&argc, &argv);
  46                 #endif
  47
  48                 m->setFileName(logFileName);
  49
  50
  51                 //version
  52                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  53                         system("clear");
  54                         #if defined (__APPLE__) || (__MACH__)
  55                                 m->mothurOutJustToLog("Mac version");
  56                                 m->mothurOutEndLine(); m->mothurOutEndLine();
  57                         #else
  58                                 m->mothurOutJustToLog("Linux version");
  59                                 m->mothurOutEndLine(); m->mothurOutEndLine();
  60                         #endif
  61
  62                 #else
  63                         system("CLS");
  64                         m->mothurOutJustToLog("Windows version");
  65                         m->mothurOutEndLine(); m->mothurOutEndLine();
  66                 #endif
  67
  68                 #ifdef USE_READLINE
  69                         m->mothurOutJustToLog("Using ReadLine");
  70                         m->mothurOutEndLine(); m->mothurOutEndLine();
  71                 #endif
  72
  73                 #ifdef MOTHUR_FILES
  74                         string temp = MOTHUR_FILES;
  75
  76                         //add / to name if needed
  77                         string lastChar = temp.substr(temp.length()-1);
  78                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  79                                 if (lastChar != "/") { temp += "/"; }
  80                         #else
  81                                 if (lastChar != "\\") { temp += "\\"; }
  82                         #endif
  83
  84                         temp = m->getFullPathName(temp);
  85                         m->setDefaultPath(temp);
  86
  87                         m->mothurOutJustToLog("Using default file location " + temp);
  88                         m->mothurOutEndLine(); m->mothurOutEndLine();
  89                 #endif
  90
  91                 #ifdef BIT_VERSION
  92                         m->mothurOutJustToLog("Running 64Bit Version");
  93                         m->mothurOutEndLine(); m->mothurOutEndLine();
  94                 #else
  95                         m->mothurOutJustToLog("Running 32Bit Version");
  96                         m->mothurOutEndLine(); m->mothurOutEndLine();
  97                 #endif
  98
  99                 //get releaseDate from Make
 100                 string releaseDate = RELEASE_DATE;
 101                 string mothurVersion = VERSION;
 102                 m->setReleaseDate(releaseDate);
 103                 m->setVersion(mothurVersion);
 104
 105                 //header
 106                 m->mothurOut("mothur v." + mothurVersion);
 107                 m->mothurOutEndLine();
 108                 m->mothurOut("Last updated: " + releaseDate);
 109                 m->mothurOutEndLine();
 110                 m->mothurOutEndLine();
 111                 m->mothurOut("by");
 112                 m->mothurOutEndLine();
 113                 m->mothurOut("Patrick D. Schloss");
 114                 m->mothurOutEndLine();
 115                 m->mothurOutEndLine();
 116                 m->mothurOut("Department of Microbiology & Immunology");
 117                 m->mothurOutEndLine();
 118                 m->mothurOut("University of Michigan");
 119                 m->mothurOutEndLine();
 120                 m->mothurOut("pschloss@umich.edu");
 121                 m->mothurOutEndLine();
 122                 m->mothurOut("http://www.mothur.org");
 123                 m->mothurOutEndLine();
 124                 m->mothurOutEndLine();
 125                 m->mothurOut("When using, please cite:");
 126                 m->mothurOutEndLine();
 127                 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.");
 128                 m->mothurOutEndLine();
 129                 m->mothurOutEndLine();
 130                 m->mothurOut("Distributed under the GNU General Public License");
 131                 m->mothurOutEndLine();
 132                 m->mothurOutEndLine();
 133                 m->mothurOut("Type 'help()' for information on the commands that are available");
 134                 m->mothurOutEndLine();
 135                 m->mothurOutEndLine();
 136                 m->mothurOut("Type 'quit()' to exit program");
 137                 m->mothurOutEndLine();
 138
 139                 #ifdef USE_MPI
 140                         m->mothurOutJustToLog("Using MPI\tversion ");
 141                         int version, subversion;
 142                         MPI_Get_version(&version, &subversion);
 143                         m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
 144                 #endif
 145
 146                 //srand(54321);
 147                 srand( (unsigned)time( NULL ) );
 148
 149                 Engine* mothur;
 150                 bool bail = 0;
 151                 string input;
 152
 153                 if(argc>1){
 154                         input = argv[1];
 155
 156                         if (input[0] == '#') {
 157                                 m->mothurOutJustToLog("Script Mode");
 158                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 159
 160                                 mothur = new ScriptEngine(argv[0], argv[1]);
 161                         }else{
 162                                 m->mothurOutJustToLog("Batch Mode");
 163                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 164
 165                                 mothur = new BatchEngine(argv[0], argv[1]);
 166                         }
 167                 }
 168                 else{
 169                         m->mothurOutJustToLog("Interactive Mode");
 170                         m->mothurOutEndLine(); m->mothurOutEndLine();
 171
 172                         mothur = new InteractEngine(argv[0]);
 173                 }
 174
 175                 while(bail == 0)        {       bail = mothur->getInput();      }
 176
 177                 //closes logfile so we can rename
 178                 m->closeLog();
 179
 180                 string outputDir = mothur->getOutputDir();
 181                 string tempLog = mothur->getLogFileName();
 182                 bool append = mothur->getAppend();
 183
 184                 string newlogFileName;
 185                 if (tempLog != "") {
 186                         newlogFileName = outputDir + tempLog;
 187
 188                         if (!append) {
 189                                 //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 190                                 rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 191
 192                         }else {
 193                                 ofstream outNewLog;
 194                                 m->openOutputFileAppend(newlogFileName, outNewLog);
 195                                 outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
 196                                 outNewLog.close();
 197
 198                                 m->appendFiles(logFileName, newlogFileName);
 199                                 remove(logFileName.c_str());
 200                         }
 201                 }else{
 202                         newlogFileName = outputDir + logFileName;
 203                         //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 204                         rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 205                 }
 206
 207
 208                 delete mothur;
 209
 210                 #ifdef USE_MPI
 211                         MPI_Finalize();
 212                 #endif
 213
 214                 return 0;
 215         }
 216         catch(exception& e) {
 217                 m->errorOut(e, "mothur", "main");
 218                 exit(1);
 219         }
 220 }
 221
 222 /**************************************************************************************************/
 223