X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=ea1c0e14dc9f89fe0157d24828a2e9552297389c;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=54197174e1fa3da14861614734b1dc58314a466a;hpb=7b80945ef716dd72d00563a5a4d692394f7f84c3;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index 5419717..ea1c0e1 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -95,14 +95,13 @@ string Engine::findMothursPath(){
 
 InteractEngine::InteractEngine(string path){
 
-	globaldata = GlobalData::getInstance();
 	
 	string temppath = path.substr(0, (path.find_last_of("othur")-5));
 	
 	//this will happen if you set the path variable to contain mothur's exe location
 	if (temppath == "") { path = findMothursPath(); }
 	
-	globaldata->argv = path;
+	mout->argv = path;
 }
 
 /***********************************************************************/
@@ -180,8 +179,20 @@ bool InteractEngine::getInput(){
 					//cout << pid << " is in execute " << commandName << endl;
 					#endif
 					//executes valid command
+					mout->runParse = true;
+					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(); }
@@ -215,7 +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);
 				}	
 				
@@ -250,7 +261,6 @@ string Engine::getCommand()  {
 //This function opens the batchfile to be used by BatchEngine::getInput.
 BatchEngine::BatchEngine(string path, string batchFileName){
 	try {
-		globaldata = GlobalData::getInstance();
 	
 		openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
 		
@@ -259,7 +269,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 		//this will happen if you set the path variable to contain mothur's exe location
 		if (temppath == "") { path = findMothursPath(); }
 		
-		globaldata->argv = path;
+		mout->argv = path;
 				
 	}
 	catch(exception& e) {
@@ -355,8 +365,21 @@ bool BatchEngine::getInput(){
 						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 					#endif
 					//executes valid command
+					mout->runParse = true;
+					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(); }
@@ -387,7 +410,7 @@ bool BatchEngine::getInput(){
 /***********************************************************************/
 string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 	try {
-		
+			
 		string nextcommand = "";
 		
 		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
@@ -406,7 +429,6 @@ string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 //This function opens the batchfile to be used by BatchEngine::getInput.
 ScriptEngine::ScriptEngine(string path, string commandString){
 	try {
-		globaldata = GlobalData::getInstance();
 		
 		//remove quotes
 		listOfCommands = commandString.substr(1, (commandString.length()-1));
@@ -416,7 +438,7 @@ ScriptEngine::ScriptEngine(string path, string commandString){
 		//this will happen if you set the path variable to contain mothur's exe location
 		if (temppath == "") { path = findMothursPath(); }
 		
-		globaldata->argv = path;
+		mout->argv = path;
 				
 	}
 	catch(exception& e) {
@@ -458,9 +480,13 @@ bool ScriptEngine::getInput(){
 			
 			if (input == "") { input = "quit()"; }
 			
-			mout->mothurOutEndLine();
-			mout->mothurOut("mothur > " + input);
-			mout->mothurOutEndLine();
+			if (mout->gui) {
+				if ((input.find("quit") != string::npos) || (input.find("set.logfile") != string::npos)) {}
+				else if ((input.find("get.current") != string::npos) && (!mout->hasCurrentFiles())) {}
+				else { mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine(); }
+			}else{
+				mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine();
+			}
 			
 			#ifdef USE_MPI
 				//send commandName
@@ -508,8 +534,20 @@ bool ScriptEngine::getInput(){
 							//cout << pid << " is in execute" << endl;	
 					#endif
 					//executes valid command
+					mout->runParse = true;
+					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(); }