#include "engine.hpp"
#include "globaldata.hpp"
-using namespace std;
+/**************************************************************************************************/
GlobalData* GlobalData::_uniqueInstance = 0;
+CommandFactory* CommandFactory::_uniqueInstance = 0;
int main(int argc, char *argv[]){
try {
+
+ string log = "mothur.logFile";
+ remove(log.c_str());
+
+ time_t ltime = time(NULL); /* calendar time */
+ string logFileName = "mothur." + toString(ltime) + ".logfile";
+
+ //version
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ system("clear");
+ #if defined (__APPLE__) || (__MACH__)
+ mothurOutJustToLog("Mac version");
+ mothurOutEndLine(); mothurOutEndLine();
+ #else
+ mothurOutJustToLog("Linux version");
+ mothurOutEndLine(); mothurOutEndLine();
+ #endif
+
+ #else
+ system("CLS");
+ mothurOutJustToLog("Windows version");
+ mothurOutEndLine(); mothurOutEndLine();
+ #endif
+
+ #ifdef USE_READLINE
+ mothurOutJustToLog("Using ReadLine");
+ mothurOutEndLine(); mothurOutEndLine();
+ #endif
+
+ //header
+ mothurOut("mothur v.1.8");
+ mothurOutEndLine();
+ mothurOut("Last updated: 2/02/2010");
+ mothurOutEndLine();
+ mothurOutEndLine();
+ mothurOut("by");
+ mothurOutEndLine();
+ mothurOut("Patrick D. Schloss");
+ mothurOutEndLine();
+ mothurOutEndLine();
+ mothurOut("Department of Microbiology & Immunology");
+ mothurOutEndLine();
+ mothurOut("University of Michigan");
+ mothurOutEndLine();
+ mothurOut("pschloss@umich.edu");
+ mothurOutEndLine();
+ mothurOut("http://www.mothur.org");
+ mothurOutEndLine();
+ mothurOutEndLine();
+ mothurOut("When using, please cite:");
+ mothurOutEndLine();
+ 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.");
+ mothurOutEndLine();
+ mothurOutEndLine();
+ mothurOut("Distributed under the GNU General Public License");
+ mothurOutEndLine();
+ mothurOutEndLine();
+ mothurOut("Type 'help()' for information on the commands that are available");
+ mothurOutEndLine();
+ mothurOutEndLine();
+ mothurOut("Type 'quit()' to exit program");
+ mothurOutEndLine();
+
+
//srand(54321);
srand( (unsigned)time( NULL ) );
-
+
Engine* mothur;
bool bail = 0;
+ string input;
if(argc>1){
- mothur = new BatchEngine(argv[1]);
+ input = argv[1];
+
+ if (input[0] == '#') {
+ mothurOutJustToLog("Script Mode");
+ mothurOutEndLine(); mothurOutEndLine();
+
+ mothur = new ScriptEngine(argv[0], argv[1]);
+ }else{
+ mothurOutJustToLog("Batch Mode");
+ mothurOutEndLine(); mothurOutEndLine();
+
+ mothur = new BatchEngine(argv[0], argv[1]);
+ }
}
else{
- mothur = new InteractEngine();
+ mothurOutJustToLog("Interactive Mode");
+ mothurOutEndLine(); mothurOutEndLine();
+
+ mothur = new InteractEngine(argv[0]);
}
-
+
while(bail == 0) { bail = mothur->getInput(); }
+
+ string outputDir = mothur->getOutputDir();
+ logFileName = outputDir + logFileName;
+ //need this because mothur.h makes the logfile, but doesn't know where to put it
+ rename(log.c_str(), logFileName.c_str()); //logfile with timestamp
+
delete mothur;
-
+
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";
+ errorOut(e, "mothur", "main");
exit(1);
}
}
+/**************************************************************************************************/
+