X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=24adcb53b59f39f049269d74b4da953a5f387262;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=d595be332eed785c27037710396d1a7dd46c845e;hpb=82bf18e3ef0a52345519f91a682e64cc385b56bb;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index d595be3..24adcb5 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -34,7 +34,7 @@ string Engine::findMothursPath(){
 		
 		//delimiting path char
 		char delim;
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			delim = ':';
 		#else
 			delim = ';';
@@ -56,7 +56,7 @@ string Engine::findMothursPath(){
 		
 		if (mothurPath != "") {
 			//add mothur so it looks like what argv would look like
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				mothurPath += "/mothur";
 			#else
 				mothurPath += "\\mothur";
@@ -71,7 +71,7 @@ string Engine::findMothursPath(){
 				//is this mothurs path?
 				ifstream in;
 				string tempIn = dirs[i];
-				#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 					tempIn += "/mothur";
 				#else
 					tempIn += "\\mothur";
@@ -180,14 +180,18 @@ bool InteractEngine::getInput(){
 					#endif
 					//executes valid command
 					mout->runParse = true;
-					mout->Groups.clear();
-					mout->namesOfGroups.clear();
+					mout->clearGroups();
+					mout->clearAllGroups();
 					mout->Treenames.clear();
-					mout->names.clear();
 					mout->saveNextLabel = "";
+					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.clear();
 							
 					Command* command = cFactory->getCommand(commandName, options);
-					quitCommandCalled = command->execute();
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
 							
 					//if we aborted command
 					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
@@ -214,14 +218,14 @@ bool InteractEngine::getInput(){
 string Engine::getCommand()  {
 	try {
 	
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			#ifdef USE_READLINE
 				char* nextCommand = NULL;
 				nextCommand = readline("mothur > ");
 				
 				if(nextCommand != NULL) {  add_history(nextCommand);  }	
 				else{ //^D causes null string and we want it to quit mothur
-					strcpy(nextCommand, "quit"); 
+					nextCommand = strdup("quit");
 					mout->mothurOut(nextCommand);
 				}	
 				
@@ -361,14 +365,19 @@ bool BatchEngine::getInput(){
 					#endif
 					//executes valid command
 					mout->runParse = true;
-					mout->Groups.clear();
-					mout->namesOfGroups.clear();
+					mout->clearGroups();
+					mout->clearAllGroups();
 					mout->Treenames.clear();
-					mout->names.clear();
 					mout->saveNextLabel = "";
+					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.clear();
+
 							
 					Command* command = cFactory->getCommand(commandName, options);
-					quitCommandCalled = command->execute();
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
 							
 					//if we aborted command
 					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
@@ -399,7 +408,7 @@ bool BatchEngine::getInput(){
 /***********************************************************************/
 string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 	try {
-		
+			
 		string nextcommand = "";
 		
 		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
@@ -524,14 +533,18 @@ bool ScriptEngine::getInput(){
 					#endif
 					//executes valid command
 					mout->runParse = true;
-					mout->Groups.clear();
-					mout->namesOfGroups.clear();
+					mout->clearGroups();
+					mout->clearAllGroups();
 					mout->Treenames.clear();
-					mout->names.clear();
 					mout->saveNextLabel = "";
-							
+					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.clear();
+
 					Command* command = cFactory->getCommand(commandName, options);
-					quitCommandCalled = command->execute();
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { quitCommandCalled = command->execute(); }
 					
 					//if we aborted command
 					if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }