MothurOut* m = MothurOut::getInstance();

ctrlc_pressed = 1;

m->control_pressed = ctrlc_pressed;

if (m->executing) { //if mid command quit execution, else quit mothur

m->mothurOutEndLine(); m->mothurOut("quitting command..."); m->mothurOutEndLine();

}else{

m->mothurOut("quitting mothur"); m->mothurOutEndLine();

exit(1);

}

MothurOut* m = MothurOut::getInstance();

try {

signal(SIGINT, ctrlc_handler );

time_t ltime = time(NULL); /* calendar time */

string logFileName = "mothur." + toString(ltime) + ".logfile";

#ifdef USE_MPI

MPI_Init(&argc, &argv);

#endif

m->setFileName(logFileName);

#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)

system("clear");

#else

system("CLS");

#endif

#ifdef MOTHUR_FILES

string temp = MOTHUR_FILES;

//add / to name if needed

string lastChar = temp.substr(temp.length()-1);

#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)

if (lastChar != "/") { temp += "/"; }

#else

if (lastChar != "\\") { temp += "\\"; }

#endif

temp = m->getFullPathName(temp);

m->setDefaultPath(temp);

#endif

#ifdef USE_MPI

int version, subversion;

MPI_Get_version(&version, &subversion);

#endif

//get releaseDate from Make

string releaseDate = RELEASE_DATE;

string mothurVersion = VERSION;

m->setReleaseDate(releaseDate);

m->setVersion(mothurVersion);

//will make the gui output "pretty"

bool outputHeader = true;

if (argc>1) {

string guiInput = argv[1];

if (guiInput[0] == '+') { outputHeader = false; }

if (guiInput[0] == '-') { outputHeader = false; }

}

if (outputHeader) {

//version

#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)

#if defined (__APPLE__) || (__MACH__)

m->mothurOutJustToLog("Mac version");

m->mothurOutEndLine(); m->mothurOutEndLine();

#else

m->mothurOutJustToLog("Linux version");

m->mothurOutEndLine(); m->mothurOutEndLine();

#endif

#else

m->mothurOutJustToLog("Windows version");

m->mothurOutEndLine(); m->mothurOutEndLine();

#endif

#ifdef USE_READLINE

m->mothurOutJustToLog("Using ReadLine");

m->mothurOutEndLine(); m->mothurOutEndLine();

#endif

#ifdef MOTHUR_FILES

m->mothurOutJustToLog("Using default file location " + temp);

m->mothurOutEndLine(); m->mothurOutEndLine();

#endif

#ifdef BIT_VERSION

m->mothurOutJustToLog("Running 64Bit Version");

m->mothurOutEndLine(); m->mothurOutEndLine();

#else

m->mothurOutJustToLog("Running 32Bit Version");

m->mothurOutEndLine(); m->mothurOutEndLine();

#endif

//header

m->mothurOut("mothur v." + mothurVersion);

m->mothurOutEndLine();

m->mothurOut("Last updated: " + releaseDate);

m->mothurOutEndLine();

m->mothurOutEndLine();

m->mothurOut("by");

m->mothurOutEndLine();

m->mothurOut("Patrick D. Schloss");

m->mothurOutEndLine();

m->mothurOutEndLine();

m->mothurOut("Department of Microbiology & Immunology");

m->mothurOutEndLine();

m->mothurOut("University of Michigan");

m->mothurOutEndLine();

m->mothurOut("pschloss@umich.edu");

m->mothurOutEndLine();

m->mothurOut("http://www.mothur.org");

m->mothurOutEndLine();

m->mothurOutEndLine();

m->mothurOut("When using, please cite:");

m->mothurOutEndLine();

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.");

m->mothurOutEndLine();

m->mothurOutEndLine();

m->mothurOut("Distributed under the GNU General Public License");

m->mothurOutEndLine();

m->mothurOutEndLine();

m->mothurOut("Type 'help()' for information on the commands that are available");

m->mothurOutEndLine();

m->mothurOutEndLine();

m->mothurOut("Type 'quit()' to exit program");

m->mothurOutEndLine();

#ifdef USE_MPI

m->mothurOutJustToLog("Using MPI\tversion ");

m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");

#endif

}

//srand(54321);

srand( (unsigned)time( NULL ) );

Engine* mothur = NULL;

bool bail = 0;

string input;

if(argc>1){

input = argv[1];

//m->mothurOut("input = " + input); m->mothurOutEndLine();

if (input[0] == '#') {

m->mothurOutJustToLog("Script Mode");

m->mothurOutEndLine(); m->mothurOutEndLine();

mothur = new ScriptEngine(argv[0], argv[1]);

}else if (input[0] == '+') {

mothur = new ScriptEngine(argv[0], argv[1]);

m->gui = true;

}else if (input == "-version") {

m->mothurOut("Mothur version=" + mothurVersion + "\nRelease Date=" + releaseDate); m->mothurOutEndLine(); m->mothurOutEndLine(); m->closeLog();

#ifdef USE_MPI

MPI_Finalize();

#endif

return 0;

}else{

m->mothurOutJustToLog("Batch Mode");

m->mothurOutEndLine(); m->mothurOutEndLine();

mothur = new BatchEngine(argv[0], argv[1]);

}

}

else{

m->mothurOutJustToLog("Interactive Mode");

m->mothurOutEndLine(); m->mothurOutEndLine();

mothur = new InteractEngine(argv[0]);

}

while(bail == 0) { bail = mothur->getInput(); }

//closes logfile so we can rename

m->closeLog();

string outputDir = mothur->getOutputDir();

string tempLog = mothur->getLogFileName();

bool append = mothur->getAppend();

string newlogFileName;

if (tempLog != "") {

newlogFileName = outputDir + tempLog;

if (!append) {

//need this because m->mothurOut makes the logfile, but doesn't know where to put it

rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp

}else {

ofstream outNewLog;

m->openOutputFileAppend(newlogFileName, outNewLog);

if (!m->gui) {

outNewLog << endl << endl << "*********************************************************************************" << endl << endl;

}else {

outNewLog << endl;

}

outNewLog.close();

m->appendFiles(logFileName, newlogFileName);

m->mothurRemove(logFileName);

}

}else{

newlogFileName = outputDir + logFileName;

//need this because m->mothurOut makes the logfile, but doesn't know where to put it

rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp

}

if (mothur != NULL) { delete mothur; }

#ifdef USE_MPI

MPI_Finalize();

#endif

return 0;

}

catch(exception& e) {

m->errorOut(e, "mothur", "main");

exit(1);

}