X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=ea1c0e14dc9f89fe0157d24828a2e9552297389c;hb=ecd4f324189cf1cb49a3eb49d5cff58562f27b7f;hp=d595be332eed785c27037710396d1a7dd46c845e;hpb=82bf18e3ef0a52345519f91a682e64cc385b56bb;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index d595be3..ea1c0e1 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -180,14 +180,19 @@ 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(); }
@@ -221,7 +226,7 @@ string Engine::getCommand()  {
 				
 				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 +366,20 @@ 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 +410,7 @@ bool BatchEngine::getInput(){
 /***********************************************************************/
 string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 	try {
-		
+			
 		string nextcommand = "";
 		
 		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
@@ -524,14 +535,19 @@ 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(); }