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
  77                         //add / to name if needed
  78                         string lastChar = temp.substr(temp.length()-1);
  79                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  80                                 if (lastChar != "/") { temp += "/"; }
  81                         #else
  82                                 if (lastChar != "\\") { temp += "\\"; }
  83                         #endif
  84
  85                         temp = getFullPathName(temp);
  86                         m->setDefaultPath(temp);
  87
  88                         m->mothurOutJustToLog("Using default file location " + temp);
  89                         m->mothurOutEndLine(); m->mothurOutEndLine();
  90                 #endif
  91
  92                 #ifdef BIT_VERSION
  93                         m->mothurOutJustToLog("Running 64Bit Version");
  94                         m->mothurOutEndLine(); m->mothurOutEndLine();
  95                 #else
  96                         m->mothurOutJustToLog("Running 32Bit Version");
  97                         m->mothurOutEndLine(); m->mothurOutEndLine();
  98                 #endif
  99
 100                 //header
 101                 m->mothurOut("mothur v.1.12.0");
 102                 m->mothurOutEndLine();
 103                 m->mothurOut("Last updated: 7/23/2010");
 104                 m->mothurOutEndLine();
 105                 m->mothurOutEndLine();
 106                 m->mothurOut("by");
 107                 m->mothurOutEndLine();
 108                 m->mothurOut("Patrick D. Schloss");
 109                 m->mothurOutEndLine();
 110                 m->mothurOutEndLine();
 111                 m->mothurOut("Department of Microbiology & Immunology");
 112                 m->mothurOutEndLine();
 113                 m->mothurOut("University of Michigan");
 114                 m->mothurOutEndLine();
 115                 m->mothurOut("pschloss@umich.edu");
 116                 m->mothurOutEndLine();
 117                 m->mothurOut("http://www.mothur.org");
 118                 m->mothurOutEndLine();
 119                 m->mothurOutEndLine();
 120                 m->mothurOut("When using, please cite:");
 121                 m->mothurOutEndLine();
 122                 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.");
 123                 m->mothurOutEndLine();
 124                 m->mothurOutEndLine();
 125                 m->mothurOut("Distributed under the GNU General Public License");
 126                 m->mothurOutEndLine();
 127                 m->mothurOutEndLine();
 128                 m->mothurOut("Type 'help()' for information on the commands that are available");
 129                 m->mothurOutEndLine();
 130                 m->mothurOutEndLine();
 131                 m->mothurOut("Type 'quit()' to exit program");
 132                 m->mothurOutEndLine();
 133
 134                 #ifdef USE_MPI
 135                         m->mothurOutJustToLog("Using MPI\tversion ");
 136                         int version, subversion;
 137                         MPI_Get_version(&version, &subversion);
 138                         m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
 139                 #endif
 140
 141                 //srand(54321);
 142                 srand( (unsigned)time( NULL ) );
 143
 144                 Engine* mothur;
 145                 bool bail = 0;
 146                 string input;
 147
 148                 if(argc>1){
 149                         input = argv[1];
 150
 151                         if (input[0] == '#') {
 152                                 m->mothurOutJustToLog("Script Mode");
 153                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 154
 155                                 mothur = new ScriptEngine(argv[0], argv[1]);
 156                         }else{
 157                                 m->mothurOutJustToLog("Batch Mode");
 158                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 159
 160                                 mothur = new BatchEngine(argv[0], argv[1]);
 161                         }
 162                 }
 163                 else{
 164                         m->mothurOutJustToLog("Interactive Mode");
 165                         m->mothurOutEndLine(); m->mothurOutEndLine();
 166
 167                         mothur = new InteractEngine(argv[0]);
 168                 }
 169
 170                 while(bail == 0)        {       bail = mothur->getInput();      }
 171
 172                 //closes logfile so we can rename
 173                 m->closeLog();
 174
 175                 string outputDir = mothur->getOutputDir();
 176                 string tempLog = mothur->getLogFileName();
 177                 bool append = mothur->getAppend();
 178
 179                 string newlogFileName;
 180                 if (tempLog != "") {
 181                         newlogFileName = outputDir + tempLog;
 182
 183                         if (!append) {
 184                                 //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 185                                 rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 186
 187                         }else {
 188                                 ofstream outNewLog;
 189                                 openOutputFileAppend(newlogFileName, outNewLog);
 190                                 outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
 191                                 outNewLog.close();
 192
 193                                 appendFiles(logFileName, newlogFileName);
 194                                 remove(logFileName.c_str());
 195                         }
 196                 }else{
 197                         newlogFileName = outputDir + logFileName;
 198                         //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 199                         rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 200                 }
 201
 202
 203                 delete mothur;
 204
 205                 #ifdef USE_MPI
 206                         MPI_Finalize();
 207                 #endif
 208
 209                 return 0;
 210         }
 211         catch(exception& e) {
 212                 m->errorOut(e, "mothur", "main");
 213                 exit(1);
 214         }
 215 }
 216
 217 /**************************************************************************************************/
 218