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 #include "referencedb.h"
  14
  15 /**************************************************************************************************/
  16
  17 CommandFactory* CommandFactory::_uniqueInstance = 0;
  18 MothurOut* MothurOut::_uniqueInstance = 0;
  19 ReferenceDB* ReferenceDB::myInstance = 0;
  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                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
  50                         system("clear");
  51                 #else
  52                         system("CLS");
  53                 #endif
  54
  55                 #ifdef MOTHUR_FILES
  56                         string temp = MOTHUR_FILES;
  57
  58                         //add / to name if needed
  59                         string lastChar = temp.substr(temp.length()-1);
  60                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
  61                                 if (lastChar != "/") { temp += "/"; }
  62                         #else
  63                                 if (lastChar != "\\") { temp += "\\"; }
  64                         #endif
  65
  66                         temp = m->getFullPathName(temp);
  67                         m->setDefaultPath(temp);
  68                 #endif
  69
  70                 #ifdef USE_MPI
  71                         int version, subversion;
  72                         MPI_Get_version(&version, &subversion);
  73                 #endif
  74
  75                 //get releaseDate from Make
  76                 string releaseDate = RELEASE_DATE;
  77                 string mothurVersion = VERSION;
  78                 m->setReleaseDate(releaseDate);
  79                 m->setVersion(mothurVersion);
  80
  81                 //will make the gui output "pretty"
  82                 bool outputHeader = true;
  83                 if (argc>1) {
  84                         string guiInput = argv[1];
  85                         if (guiInput[0] == '+') { outputHeader = false; }
  86                         if (guiInput[0] == '-') { outputHeader = false; }
  87                 }
  88
  89                 if (outputHeader)  {
  90                         //version
  91                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
  92                                 #if defined (__APPLE__) || (__MACH__)
  93                                         m->mothurOutJustToLog("Mac version");
  94                                         m->mothurOutEndLine(); m->mothurOutEndLine();
  95                                 #else
  96                                         m->mothurOutJustToLog("Linux version");
  97                                         m->mothurOutEndLine(); m->mothurOutEndLine();
  98                                 #endif
  99
 100                         #else
 101                                 m->mothurOutJustToLog("Windows version");
 102                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 103                         #endif
 104
 105                         #ifdef USE_READLINE
 106                                 m->mothurOutJustToLog("Using ReadLine");
 107                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 108                         #endif
 109
 110                         #ifdef MOTHUR_FILES
 111                                 m->mothurOutJustToLog("Using default file location " + temp);
 112                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 113                         #endif
 114
 115                         #ifdef BIT_VERSION
 116                                 m->mothurOutJustToLog("Running 64Bit Version");
 117                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 118                         #else
 119                                 m->mothurOutJustToLog("Running 32Bit Version");
 120                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 121                         #endif
 122
 123                         //header
 124                         m->mothurOut("mothur v." + mothurVersion);
 125                         m->mothurOutEndLine();
 126                         m->mothurOut("Last updated: " + releaseDate);
 127                         m->mothurOutEndLine();
 128                         m->mothurOutEndLine();
 129                         m->mothurOut("by");
 130                         m->mothurOutEndLine();
 131                         m->mothurOut("Patrick D. Schloss");
 132                         m->mothurOutEndLine();
 133                         m->mothurOutEndLine();
 134                         m->mothurOut("Department of Microbiology & Immunology");
 135                         m->mothurOutEndLine();
 136                         m->mothurOut("University of Michigan");
 137                         m->mothurOutEndLine();
 138                         m->mothurOut("pschloss@umich.edu");
 139                         m->mothurOutEndLine();
 140                         m->mothurOut("http://www.mothur.org");
 141                         m->mothurOutEndLine();
 142                         m->mothurOutEndLine();
 143                         m->mothurOut("When using, please cite:");
 144                         m->mothurOutEndLine();
 145                         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.");
 146                         m->mothurOutEndLine();
 147                         m->mothurOutEndLine();
 148                         m->mothurOut("Distributed under the GNU General Public License");
 149                         m->mothurOutEndLine();
 150                         m->mothurOutEndLine();
 151                         m->mothurOut("Type 'help()' for information on the commands that are available");
 152                         m->mothurOutEndLine();
 153                         m->mothurOutEndLine();
 154                         m->mothurOut("Type 'quit()' to exit program");
 155                         m->mothurOutEndLine();
 156
 157                         #ifdef USE_MPI
 158                                 m->mothurOutJustToLog("Using MPI\tversion ");
 159                                 m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
 160                         #endif
 161                 }
 162
 163                 //srand(54321);
 164                 srand( (unsigned)time( NULL ) );
 165
 166                 Engine* mothur = NULL;
 167                 bool bail = 0;
 168                 string input;
 169
 170                 if(argc>1){
 171                         input = argv[1];
 172                         //m->mothurOut("input = " + input); m->mothurOutEndLine();
 173
 174                         if (input[0] == '#') {
 175                                 m->mothurOutJustToLog("Script Mode");
 176                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 177
 178                                 mothur = new ScriptEngine(argv[0], argv[1]);
 179                         }else if (input[0] == '+') {
 180                                         mothur = new ScriptEngine(argv[0], argv[1]);
 181                                         m->gui = true;
 182                         }else if (input == "-version") {
 183                                 m->mothurOut("Mothur version=" + mothurVersion + "\nRelease Date=" + releaseDate); m->mothurOutEndLine(); m->mothurOutEndLine(); m->closeLog();
 184                                 #ifdef USE_MPI
 185                                         MPI_Finalize();
 186                                 #endif
 187                                 return 0;
 188                         }else{
 189                                 m->mothurOutJustToLog("Batch Mode");
 190                                 m->mothurOutEndLine(); m->mothurOutEndLine();
 191
 192                                 mothur = new BatchEngine(argv[0], argv[1]);
 193                         }
 194                 }
 195                 else{
 196                         m->mothurOutJustToLog("Interactive Mode");
 197                         m->mothurOutEndLine(); m->mothurOutEndLine();
 198
 199                         mothur = new InteractEngine(argv[0]);
 200                 }
 201
 202                 while(bail == 0)        {       bail = mothur->getInput();      }
 203
 204                 //closes logfile so we can rename
 205                 m->closeLog();
 206
 207                 string outputDir = mothur->getOutputDir();
 208                 string tempLog = mothur->getLogFileName();
 209                 bool append = mothur->getAppend();
 210
 211                 string newlogFileName;
 212                 if (tempLog != "") {
 213                         newlogFileName = outputDir + tempLog;
 214
 215                         if (!append) {
 216                                 //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 217                                 rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 218
 219                         }else {
 220                                 ofstream outNewLog;
 221                                 m->openOutputFileAppend(newlogFileName, outNewLog);
 222
 223                                 if (!m->gui) {
 224                                         outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
 225                                 }else {
 226                                         outNewLog << endl;
 227                                 }
 228                                 outNewLog.close();
 229
 230                                 m->appendFiles(logFileName, newlogFileName);
 231                                 m->mothurRemove(logFileName);
 232                         }
 233                 }else{
 234                         newlogFileName = outputDir + logFileName;
 235                         //need this because m->mothurOut makes the logfile, but doesn't know where to put it
 236                         rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
 237                 }
 238
 239
 240                 if (mothur != NULL) { delete mothur; }
 241
 242                 #ifdef USE_MPI
 243                         MPI_Finalize();
 244                 #endif
 245
 246                 return 0;
 247         }
 248         catch(exception& e) {
 249                 m->errorOut(e, "mothur", "main");
 250                 exit(1);
 251         }
 252 }
 253
 254 /**************************************************************************************************/
 255