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