int main(int argc, char **argv) {
MothurOut* m; m = MothurOut::getInstance();
string pathname = m->mothurProgramPath;
if (pathname != "") {
//add / to name if needed
string lastChar = pathname.substr(pathname.length()-1);
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if (lastChar != "/") { pathname += "/TestMothur/TestFiles/"; }
#else
if (lastChar != "\\") { pathname += "\\TestMothur\\TestFiles\\"; }
#endif
}
m->setTestFilePath(pathname);
::testing::InitGoogleTest(&argc, argv);
return RUN_ALL_TESTS();
}
void ctrlc_handler ( int sig ) {
MothurOut* m = MothurOut::getInstance();
ctrlc_pressed = 1;
m->setControl_pressed(ctrlc_pressed);
if (m->getExecuting()) { //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);
}
}
int main(int argc, char *argv[]){
MothurOut* m = MothurOut::getInstance();
try {
CurrentFile* current = CurrentFile::getInstance();
Utils util;
bool createLogFile = true;
signal(SIGINT, ctrlc_handler );
#if defined NON_WINDOWS
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 (lastChar != PATH_SEPARATOR) { temp += PATH_SEPARATOR; }
temp = util.getFullPathName(temp);
current->setDefaultPath(temp);
#endif
#ifdef LOGFILE_NAME
string logfilename = LOGFILE_NAME;
logfilename = util.getFullPathName(logfilename);
m->appendLogBuffer("Using Static Logfile " + logfilename + "\n");
m->setLogFileName(logfilename, false);
m->mothurOut("\n");
#endif
string releaseDate = "";
#ifdef RELEASE_DATE
releaseDate = RELEASE_DATE;
#else
string year, month, day;
util.getCurrentDate(year, month, day);
releaseDate = month + "/" + day + "/" + year;
#endif
//get releaseDate from Make
string mothurVersion = VERSION;
current->setReleaseDate(releaseDate);
current->setVersion(mothurVersion);
//will make the gui output "pretty"
bool outputHeader = true;
if (argc>1) {
if (argc > 2) { //is one of these -q for quiet mode?
if (argc > 3) { m->appendLogBuffer("[ERROR]: mothur only allows command inputs and the -q command line options.\n i.e. ./mothur \"#summary.seqs(fasta=final.fasta);\" -q\n or ./mothur -q \"#summary.seqs(fasta=final.fasta);\"\n"); return 0; }
else {
string argv1 = argv[1];
string argv2 = argv[2];
if ((argv1 == "--quiet") || (argv1 == "-q")) {
m->setQuietMode(true);
argv[1] = argv[2];
}else if ((argv2 == "--quiet") || (argv2 == "-q")) {
m->setQuietMode(true);
}else {
m->appendLogBuffer("[ERROR]: mothur only allows command inputs and the -q command line options.\n");
m->appendLogBuffer("[ERROR]: Unrecognized options: " + argv1 + " " + argv2 + "\n");
return 0;
}
}
}
}
if (outputHeader) {
//version
#if defined NON_WINDOWS
#if defined (__APPLE__) || (__MACH__)
m->appendLogBuffer("Mac version\n\n");
#else
m->appendLogBuffer("Linux version\n\n");
#endif
#else
m->appendLogBuffer("Windows version\n\n");
#endif
string packagesUsed = "";
#ifdef USE_READLINE
packagesUsed += "ReadLine,";
#endif
#ifdef USE_BOOST
packagesUsed += "Boost,";
#endif
#ifdef USE_HDF5
packagesUsed += "HDF5,";
#endif
if (packagesUsed != "") {
//remove last comma
packagesUsed = packagesUsed.substr(0,packagesUsed.length()-1);
m->appendLogBuffer("Using " + packagesUsed + "\n");
}
#ifdef MOTHUR_FILES
m->appendLogBuffer("\nUsing default file location " + temp + "\n\n");
#endif
//header
m->appendLogBuffer("mothur v." + mothurVersion + "\n");
m->appendLogBuffer("Last updated: " + releaseDate + "\n");
m->appendLogBuffer("by\n");
m->appendLogBuffer("Patrick D. Schloss\n\n");
m->appendLogBuffer("Department of Microbiology & Immunology\n\n");
m->appendLogBuffer("University of Michigan\n");
m->appendLogBuffer("http://www.mothur.org\n\n");
m->appendLogBuffer("When using, please cite:\n");
m->appendLogBuffer("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.\n\n");
m->appendLogBuffer("Distributed under the GNU General Public License\n\n");
m->appendLogBuffer("Type 'help()' for information on the commands that are available\n\n");
m->appendLogBuffer("For questions and analysis support, please visit our forum at https://forum.mothur.org\n\n");
m->appendLogBuffer("Type 'quit()' to exit program\n\n");
}
m->setRandomSeed(19760620);
m->appendLogBuffer("[NOTE]: Setting random seed to 19760620.\n\n");
Engine* mothur = NULL;
bool bail = 0;
string input;
if(argc>1){
input = argv[1];
if (input[0] == '#') {
m->appendLogBuffer("Script Mode\n\n");
mothur = new ScriptEngine(argv[0], argv[1]);
}else if ((input == "--version") || (input == "-v")) {
createLogFile = false;
string OS = "";
//version
#if defined NON_WINDOWS
#if defined (__APPLE__) || (__MACH__)
OS = "Mac ";
#else
OS = "Linux ";
#endif
#else
OS = "Windows ";
#endif
cout << (OS + "\nMothur version=" + mothurVersion + "\nRelease Date=" + releaseDate + "\n\n");
return 0;
}else if ((input == "--help") || (input == "-h")) {
createLogFile = false;
m->appendLogBuffer("Script Mode\n\n");
char* temp = new char[16];
*temp = '\0'; strncat(temp, "#help();quit();", 15);
argv[1] = temp;
mothur = new ScriptEngine(argv[0], argv[1]);
}else{
m->appendLogBuffer("Batch Mode\n\n");
mothur = new BatchEngine(argv[0], argv[1]);
}
}else{
m->appendLogBuffer("Interactive Mode\n\n");
mothur = new InteractEngine(argv[0]);
}
while(bail == 0) { bail = mothur->getInput(); }
string newlogFileName = mothur->getLogFileName();
if (!createLogFile) { util.mothurRemove(newlogFileName); }
if (mothur != NULL) { delete mothur; }
int returnCode = 0;
if (m->getNumErrors() != 0) { returnCode = 1; }
m->closeLog();
return returnCode;
}
catch(exception& e) {
m->errorOut(e, "mothur", "main");
exit(1);
}
}
int main(int argc, char *argv[]){
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("*****@*****.**");
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);
}
}