X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothur.cpp;h=accdb2962c198988c457dc8f837b8817dc2799f0;hp=8c55240965b5481bae5a551488c6e3ac957ee494;hb=615301e57c25e241356a9c2380648d117709458d;hpb=c25c956e4a3c7ca3271d48ee6215c72b2ec80c44 diff --git a/mothur.cpp b/mothur.cpp index 8c55240..accdb29 100644 --- a/mothur.cpp +++ b/mothur.cpp @@ -9,40 +9,247 @@ #include "mothur.h" #include "engine.hpp" -#include "globaldata.hpp" +#include "mothurout.h" +#include "referencedb.h" -using namespace std; - -GlobalData* GlobalData::_uniqueInstance = 0; +/**************************************************************************************************/ +CommandFactory* CommandFactory::_uniqueInstance = 0; +MothurOut* MothurOut::_uniqueInstance = 0; +ReferenceDB* ReferenceDB::myInstance = 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 { + 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) || (__linux__) || (__unix__) || (__unix) + 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) || (__linux__) || (__unix__) || (__unix) + 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) || (__linux__) || (__unix__) || (__unix) + #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; + + Engine* mothur = NULL; bool bail = 0; - + string input; + if(argc>1){ - mothur = new BatchEngine(argv[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{ - mothur = 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 = mothur->getInput(); } - - delete mothur; - + }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) { - 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); } } +/**************************************************************************************************/ +