X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.cpp;h=c9914229c9d41c72da266a46d5f26516e0f60fe4;hb=19fcbbdba99658f5eca244803280f9ee7f9f6607;hp=45be11d8adbb0a74fa5412298e803991f1877fd9;hpb=9d6f36294dcaef3ac65a0e69fd8140077c3209e0;p=mothur.git

diff --git a/mothur.cpp b/mothur.cpp
index 45be11d..c991422 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -9,14 +9,14 @@
  
 #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 ) {
@@ -79,13 +79,14 @@ 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__)
@@ -162,13 +163,13 @@ int main(int argc, char *argv[]){
 		//srand(54321);
 		srand( (unsigned)time( NULL ) );
 		
-		Engine* mothur;
+		Engine* mothur = NULL;
 		bool bail = 0;
 		string input;
  
 		if(argc>1){
 			input = argv[1];
-			m->mothurOut("input = " + input); m->mothurOutEndLine();
+			//m->mothurOut("input = " + input); m->mothurOutEndLine();
 
 			if (input[0] == '#') {
 				m->mothurOutJustToLog("Script Mode");
@@ -178,6 +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();
@@ -215,11 +222,13 @@ int main(int argc, char *argv[]){
 				
 				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;
@@ -228,7 +237,7 @@ int main(int argc, char *argv[]){
 		}
 		
 				
-		delete mothur;
+		if (mothur != NULL) { delete mothur; }
 		
 		#ifdef USE_MPI
 			MPI_Finalize();