X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=ad7a7ad73ad03660976137117b15035d2d2b4757;hb=5d6d303e481489e226fdf8d6c5385b99b50718bc;hp=fbf986dc6965de7d9d269c31f35e99ed85467a9d;hpb=11c115c802602be50e106aae56969e15d2c49a62;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index fbf986d..ad7a7ad 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -49,7 +49,7 @@ InteractEngine::InteractEngine(string path){
 		
 		//break apart path variable by ':'
 		vector<string> dirs;
-		splitAtChar(envPath, dirs, delim);
+		mout->splitAtChar(envPath, dirs, delim);
 		
 		//get path related to mothur
 		string mothurPath = "";
@@ -181,7 +181,7 @@ string Engine::getCommand()  {
 				
 				if(nextCommand != NULL) {  add_history(nextCommand);  }	
 				else{ //^D causes null string and we want it to quit mothur
-					nextCommand = "quit"; 
+					strcpy(nextCommand, "quit"); 
 					mout->mothurOut(nextCommand);
 				}	
 				
@@ -218,7 +218,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 	try {
 		globaldata = GlobalData::getInstance();
 	
-		openedBatch = openInputFile(batchFileName, inputBatchFile);
+		openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
 		
 		string temppath = path.substr(0, (path.find_last_of('m')));
 	
@@ -237,7 +237,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 			
 			//break apart path variable by ':'
 			vector<string> dirs;
-			splitAtChar(envPath, dirs, delim);
+			mout->splitAtChar(envPath, dirs, delim);
 			
 			//get path related to mothur
 			string mothurPath = "";
@@ -370,7 +370,7 @@ bool BatchEngine::getInput(){
 				}
 				
 			}
-			gobble(inputBatchFile);
+			mout->gobble(inputBatchFile);
 		}
 		
 		inputBatchFile.close();
@@ -388,7 +388,7 @@ string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 		string nextcommand = "";
 		
 		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
-		else { nextcommand = getline(inputBatchFile); }
+		else { nextcommand = mout->getline(inputBatchFile); }
 		
 		return nextcommand;
 	}
@@ -425,7 +425,7 @@ ScriptEngine::ScriptEngine(string path, string commandString){
 			
 			//break apart path variable by ':'
 			vector<string> dirs;
-			splitAtChar(envPath, dirs, delim);
+			mout->splitAtChar(envPath, dirs, delim);
 			
 			//get path related to mothur
 			string mothurPath = "";
@@ -531,7 +531,6 @@ bool ScriptEngine::getInput(){
 					mout->executing = true;
 					#ifdef USE_MPI
 						int pid, numProcesses;
-						MPI_Status status; 
 						
 						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
 						MPI_Comm_size(MPI_COMM_WORLD, &numProcesses); 
@@ -571,11 +570,16 @@ string ScriptEngine::getNextCommand(string& commandString) {
 		
 		string nextcommand = "";
 		int count = 0;
+		bool ignoreSemiColons = false;
 		
 		//go through string until you reach ; or end
 		while (count < commandString.length()) { 
 			
-			if (commandString[count] == ';') {  break;   }
+			 //you want to ignore any ; until you reach the next '
+			if ((commandString[count] == '\'') && (!ignoreSemiColons)) {  ignoreSemiColons = true;  } 
+			else if ((commandString[count] == '\'') && (ignoreSemiColons)) {  ignoreSemiColons = false;  } 
+				
+			if ((commandString[count] == ';') && (!ignoreSemiColons)) {  break;   }
 			else {		nextcommand += commandString[count];	}
 			
 			count++;