#include "mothur.h"
#include "engine.hpp"
#include "globaldata.hpp"
+#include "mothurout.h"
-using namespace std;
+/**************************************************************************************************/
GlobalData* GlobalData::_uniqueInstance = 0;
+CommandFactory* CommandFactory::_uniqueInstance = 0;
+MothurOut* MothurOut::_uniqueInstance = 0;
+/***********************************************************************/
+volatile int ctrlc_pressed = 0;
+void ctrlc_handler ( int sig ) {
+ 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[]){
- try {
- // srand(54321);
- srand( (unsigned)time( NULL ) );
+ 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
- Engine* dotur;
- bool bail = 0;
+ m->setFileName(logFileName);
+
+
+ //version
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ system("clear");
+ #if defined (__APPLE__) || (__MACH__)
+ m->mothurOutJustToLog("Mac version");
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+ #else
+ m->mothurOutJustToLog("Linux version");
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+ #endif
+ #else
+ system("CLS");
+ m->mothurOutJustToLog("Windows version");
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+ #endif
+
+ #ifdef USE_READLINE
+ m->mothurOutJustToLog("Using ReadLine");
+ 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." + 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 ");
+ 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){
- dotur = new BatchEngine(argv[1]);
+ input = argv[1];
+
+ if (input[0] == '#') {
+ m->mothurOutJustToLog("Script Mode");
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+
+ mothur = new ScriptEngine(argv[0], argv[1]);
+ }else{
+ m->mothurOutJustToLog("Batch Mode");
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+
+ mothur = new BatchEngine(argv[0], argv[1]);
+ }
}
else{
- dotur = new InteractEngine();
+ 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
- while(bail == 0) { bail = dotur->getInput(); }
-
- delete dotur;
-
+ }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) {
- cout << "Standard Error: " << e.what() << " has occurred in the dotur class Function main. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the dotur class function main. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "mothur", "main");
exit(1);
}
}
+/**************************************************************************************************/
+