X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothur.cpp;h=accdb2962c198988c457dc8f837b8817dc2799f0;hp=67ede87039d783c71a40a0317d3a1ccbffdc7b97;hb=615301e57c25e241356a9c2380648d117709458d;hpb=82bf18e3ef0a52345519f91a682e64cc385b56bb

diff --git a/mothur.cpp b/mothur.cpp
index 67ede87..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 += "\\"; }	
@@ -78,15 +79,16 @@ int main(int argc, char *argv[]){
 		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();
@@ -161,7 +163,7 @@ int main(int argc, char *argv[]){
 		//srand(54321);
 		srand( (unsigned)time( NULL ) );
 		
-		Engine* mothur;
+		Engine* mothur = NULL;
 		bool bail = 0;
 		string input;
  
@@ -177,6 +179,12 @@ int main(int argc, char *argv[]){
 			}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();
@@ -220,7 +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;
@@ -229,7 +237,7 @@ int main(int argc, char *argv[]){
 		}
 		
 				
-		delete mothur;
+		if (mothur != NULL) { delete mothur; }
 		
 		#ifdef USE_MPI
 			MPI_Finalize();