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 "mothurout.h"
  13
  14 /**************************************************************************************************/
  15
  16 CommandFactory* CommandFactory::_uniqueInstance = 0;
  17 MothurOut* MothurOut::_uniqueInstance = 0;
  18
  19 /***********************************************************************/
  20 volatile int ctrlc_pressed = 0;
  21 void ctrlc_handler ( int sig ) {
  22         MothurOut* m = MothurOut::getInstance();
  23     ctrlc_pressed = 1;
  24         m->control_pressed = ctrlc_pressed;
  25
  26         if (m->executing) { //if mid command quit execution, else quit mothur
  27                 m->mothurOutEndLine(); m->mothurOut("quitting command...");  m->mothurOutEndLine();
  28         }else{
  29                 m->mothurOut("quitting mothur");  m->mothurOutEndLine();
  30                 exit(1);
  31         }
  32 }
  33 /***********************************************************************/
  34 int main(int argc, char *argv[]){
  35         MothurOut* m = MothurOut::getInstance();
  36         try {
  37                 signal(SIGINT, ctrlc_handler );
  38
  39                 time_t ltime = time(NULL); /* calendar time */
  40                 string logFileName = "mothur." + toString(ltime) + ".logfile";
  41
  42                 #ifdef USE_MPI
  43                         MPI_Init(&argc, &argv);
  44                 #endif
  45
  46                 m->setFileName(logFileName);
  47
  48                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  49                         system("clear");
  50                 #else
  51                         system("CLS");
  52                 #endif
  53
  54                 #ifdef MOTHUR_FILES
  55                         string temp = MOTHUR_FILES;
  56
  57                         //add / to name if needed
  58                         string lastChar = temp.substr(temp.length()-1);
  59                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  60                                 if (lastChar != "/") { temp += "/"; }
  61                         #else
  62                                 if (lastChar != "\\") { temp += "\\"; }
  63                         #endif
  64
  65                         temp = m->getFullPathName(temp);
  66                         m->setDefaultPath(temp);
  67                 #endif
  68
  69                 #ifdef USE_MPI
  70                         int version, subversion;
  71                         MPI_Get_version(&version, &subversion);
  72                 #endif
  73
  74                 //get releaseDate from Make
  75                 string releaseDate = RELEASE_DATE;
  76                 string mothurVersion = VERSION;
  77                 m->setReleaseDate(releaseDate);
  78                 m->setVersion(mothurVersion);
  79
  80                 //will make the gui output "pretty"
  81                 bool guiMode = false;
  82                 if (argc>1) {
  83                         string guiInput = argv[1];
  84                         if (guiInput[0] == '+') { guiMode = true; }
  85                 }
  86
  87                 if (!guiMode) {
  88                         //version
  89                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  90                                 #if defined (__APPLE__) || (__MACH__)
  91                                         m->mothurOutJustToLog("Mac version");
  92                                         m->mothurOutEndLine(); m->mothurOutEndLine();
  93                                 #else
  94                                         m->mothurOutJustToLog("Linux version");
  95                                         m->mothurOutEndLine(); m->mothurOutEndLine();
  96                                 #endif
  97
  98                         #else
  99                                 m->mothurOutJustToLog("Windows version");
 100                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 101                         #endif
 102
 103                         #ifdef USE_READLINE
 104                                 m->mothurOutJustToLog("Using ReadLine");
 105                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 106                         #endif
 107
 108                         #ifdef MOTHUR_FILES
 109                                 m->mothurOutJustToLog("Using default file location " + temp);
 110                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 111                         #endif
 112
 113                         #ifdef BIT_VERSION
 114                                 m->mothurOutJustToLog("Running 64Bit Version");
 115                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 116                         #else
 117                                 m->mothurOutJustToLog("Running 32Bit Version");
 118                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 119                         #endif
 120
 121                         //header
 122                         m->mothurOut("mothur v." + mothurVersion);
 123                         m->mothurOutEndLine();
 124                         m->mothurOut("Last updated: " + releaseDate);
 125                         m->mothurOutEndLine();
 126                         m->mothurOutEndLine();
 127                         m->mothurOut("by");
 128                         m->mothurOutEndLine();
 129                         m->mothurOut("Patrick D. Schloss");
 130                         m->mothurOutEndLine();
 131                         m->mothurOutEndLine();
 132                         m->mothurOut("Department of Microbiology & Immunology");
 133                         m->mothurOutEndLine();
 134                         m->mothurOut("University of Michigan");
 135                         m->mothurOutEndLine();
 136                         m->mothurOut("pschloss@umich.edu");
 137                         m->mothurOutEndLine();
 138                         m->mothurOut("http://www.mothur.org");
 139                         m->mothurOutEndLine();
 140                         m->mothurOutEndLine();
 141                         m->mothurOut("When using, please cite:");
 142                         m->mothurOutEndLine();
 143                         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.");
 144                         m->mothurOutEndLine();
 145                         m->mothurOutEndLine();
 146                         m->mothurOut("Distributed under the GNU General Public License");
 147                         m->mothurOutEndLine();
 148                         m->mothurOutEndLine();
 149                         m->mothurOut("Type 'help()' for information on the commands that are available");
 150                         m->mothurOutEndLine();
 151                         m->mothurOutEndLine();
 152                         m->mothurOut("Type 'quit()' to exit program");
 153                         m->mothurOutEndLine();
 154
 155                         #ifdef USE_MPI
 156                                 m->mothurOutJustToLog("Using MPI\tversion ");
 157                                 m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
 158                         #endif
 159                 }
 160
 161                 //srand(54321);
 162                 srand( (unsigned)time( NULL ) );
 163
 164                 Engine* mothur;
 165                 bool bail = 0;
 166                 string input;
 167
 168                 if(argc>1){
 169                         input = argv[1];
 170                         //m->mothurOut("input = " + input); m->mothurOutEndLine();
 171
 172                         if (input[0] == '#') {
 173                                 m->mothurOutJustToLog("Script Mode");
 174                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 175
 176                                 mothur = new ScriptEngine(argv[0], argv[1]);
 177                         }else if (input[0] == '+') {
 178                                         mothur = new ScriptEngine(argv[0], argv[1]);
 179                                         m->gui = true;
 180                         }else{
 181                                 m->mothurOutJustToLog("Batch Mode");
 182                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 183
 184                                 mothur = new BatchEngine(argv[0], argv[1]);
 185                         }
 186                 }
 187                 else{
 188                         m->mothurOutJustToLog("Interactive Mode");
 189                         m->mothurOutEndLine(); m->mothurOutEndLine();
 190
 191                         mothur = new InteractEngine(argv[0]);
 192                 }
 193
 194                 while(bail == 0)        {       bail = mothur->getInput();      }
 195
 196                 //closes logfile so we can rename
 197                 m->closeLog();
 198
 199                 string outputDir = mothur->getOutputDir();
 200                 string tempLog = mothur->getLogFileName();
 201                 bool append = mothur->getAppend();
 202
 203                 string newlogFileName;
 204                 if (tempLog != "") {
 205                         newlogFileName = outputDir + tempLog;
 206
 207                         if (!append) {
 208                                 //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 209                                 rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 210
 211                         }else {
 212                                 ofstream outNewLog;
 213                                 m->openOutputFileAppend(newlogFileName, outNewLog);
 214
 215                                 if (!m->gui) {
 216                                         outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
 217                                 }else {
 218                                         outNewLog << endl;
 219                                 }
 220                                 outNewLog.close();
 221
 222                                 m->appendFiles(logFileName, newlogFileName);
 223                                 remove(logFileName.c_str());
 224                         }
 225                 }else{
 226                         newlogFileName = outputDir + logFileName;
 227                         //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 228                         rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 229                 }
 230
 231
 232                 delete mothur;
 233
 234                 #ifdef USE_MPI
 235                         MPI_Finalize();
 236                 #endif
 237
 238                 return 0;
 239         }
 240         catch(exception& e) {
 241                 m->errorOut(e, "mothur", "main");
 242                 exit(1);
 243         }
 244 }
 245
 246 /**************************************************************************************************/
 247