X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothur.cpp;h=accdb2962c198988c457dc8f837b8817dc2799f0;hp=b551302646c10b813740516eaa65cc46453b4a1d;hb=615301e57c25e241356a9c2380648d117709458d;hpb=836150c0a3666899ad58426388f4999d6cf8829a

diff --git a/mothur.cpp b/mothur.cpp
index b551302..accdb29 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -10,12 +10,13 @@
 #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 ) {
@@ -45,7 +46,7 @@ int main(int argc, char *argv[]){
 
 		m->setFileName(logFileName);
 		
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			system("clear");
 		#else
 			system("CLS");
@@ -56,7 +57,7 @@ int main(int argc, char *argv[]){
 		
 			//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 += "\\"; }	
@@ -87,7 +88,7 @@ int main(int argc, char *argv[]){
 		
 		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();
@@ -227,7 +228,7 @@ int main(int argc, char *argv[]){
 				outNewLog.close();
 				
 				m->appendFiles(logFileName, newlogFileName);
-				remove(logFileName.c_str());
+				m->mothurRemove(logFileName);
 			}
 		}else{  
 			newlogFileName = outputDir + logFileName;