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/*
* interface.cpp
*
*
* Created by Pat Schloss on 8/14/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
*/
#include "mothur.h"
#include "engine.hpp"
#include "mothurout.h"
#include "referencedb.h"
/**************************************************************************************************/
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[]){
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 = 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);
}
}
/**************************************************************************************************/
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