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);
+ }
}
/***********************************************************************/
int main(int argc, char *argv[]){
MothurOut* m = MothurOut::getInstance();
- try {
-
+ 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);
+
//version
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
system("clear");
m->mothurOutEndLine(); m->mothurOutEndLine();
#else
m->mothurOutJustToLog("Linux version");
- >m->mothurOutEndLine(); m->mothurOutEndLine();
+ m->mothurOutEndLine(); m->mothurOutEndLine();
#endif
#else
m->mothurOutEndLine(); m->mothurOutEndLine();
#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);
+
+ 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
+
+ //get releaseDate from Make
+ string releaseDate = RELEASE_DATE;
+ string mothurVersion = VERSION;
+ m->setReleaseDate(releaseDate);
+ m->setVersion(mothurVersion);
+
//header
- m->mothurOut("mothur v.1.8");
+ m->mothurOut("mothur v." + mothurVersion);
m->mothurOutEndLine();
- m->mothurOut("Last updated: 2/02/2010");
+ m->mothurOut("Last updated: " + releaseDate);
m->mothurOutEndLine();
m->mothurOutEndLine();
m->mothurOut("by");
m->mothurOutEndLine();
m->mothurOut("Type 'quit()' to exit program");
m->mothurOutEndLine();
-
-
+
+ #ifdef USE_MPI
+ m->mothurOutJustToLog("Using MPI\tversion ");
+ int version, subversion;
+ MPI_Get_version(&version, &subversion);
+ m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
+ #endif
+
//srand(54321);
srand( (unsigned)time( NULL ) );
Engine* mothur;
bool bail = 0;
string input;
-
+
if(argc>1){
input = argv[1];
mothur = new InteractEngine(argv[0]);
}
- while(bail == 0) { bail = mothur->getInput(); }
+ while(bail == 0) { bail = mothur->getInput(); }
+
+ //closes logfile so we can rename
+ m->closeLog();
string outputDir = mothur->getOutputDir();
- string 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
+ string tempLog = mothur->getLogFileName();
+ bool append = mothur->getAppend();
- delete mothur;
+ 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);
+ outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
+ outNewLog.close();
+
+ m->appendFiles(logFileName, newlogFileName);
+ remove(logFileName.c_str());
+ }
+ }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
+ }
+
+
+ delete mothur;
+
+ #ifdef USE_MPI
+ MPI_Finalize();
+ #endif
+
return 0;
}
catch(exception& e) {