#include "mothur.h"
#include "engine.hpp"
-#include "globaldata.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 ) {
m->setFileName(logFileName);
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
system("clear");
#else
system("CLS");
//add / to name if needed
string lastChar = temp.substr(temp.length()-1);
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if (lastChar != "/") { temp += "/"; }
#else
if (lastChar != "\\") { temp += "\\"; }
m->setVersion(mothurVersion);
//will make the gui output "pretty"
- bool guiMode = false;
+ bool outputHeader = true;
if (argc>1) {
string guiInput = argv[1];
- if (guiInput[0] == '+') { guiMode = true; }
+ if (guiInput[0] == '+') { outputHeader = false; }
+ if (guiInput[0] == '-') { outputHeader = false; }
}
- if (!guiMode) {
+ if (outputHeader) {
//version
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#if defined (__APPLE__) || (__MACH__)
m->mothurOutJustToLog("Mac version");
m->mothurOutEndLine(); m->mothurOutEndLine();
//srand(54321);
srand( (unsigned)time( NULL ) );
- Engine* mothur;
+ Engine* mothur = NULL;
bool bail = 0;
string input;
}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();
if (!m->gui) {
outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
+ }else {
+ outNewLog << endl;
}
outNewLog.close();
m->appendFiles(logFileName, newlogFileName);
- remove(logFileName.c_str());
+ m->mothurRemove(logFileName);
}
}else{
newlogFileName = outputDir + logFileName;
}
- delete mothur;
+ if (mothur != NULL) { delete mothur; }
#ifdef USE_MPI
MPI_Finalize();