X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=9e5801b1b057b2f2a1cc4a986e105ae3e73f14b5;hb=5c80ce8b80938d41cf6c64a017fa6fd50d45de5b;hp=593c2c3128d08cfe8abddfa81a1e384a1d17aa62;hpb=c82900be3ceed3d9bc491bdc98b1819ef85c1af7;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index 593c2c3..9e5801b 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -18,9 +18,10 @@
 Engine::Engine(){
 	try {
 		cFactory = CommandFactory::getInstance();
+		mout = MothurOut::getInstance();
 	}
 	catch(exception& e) {
-		errorOut(e, "Engine", "Engine");
+		mout->errorOut(e, "Engine", "Engine");
 		exit(1);
 	}
 }
@@ -31,6 +32,7 @@ InteractEngine::InteractEngine(string path){
 
 	globaldata = GlobalData::getInstance();
 	globaldata->argv = path;
+	
 }
 
 /***********************************************************************/
@@ -49,9 +51,12 @@ bool InteractEngine::getInput(){
 		
 		while(quitCommandCalled != 1){
 
-			mothurOutEndLine();
+			mout->mothurOutEndLine();
+			
+			input = getCommand();	
+			mout->mothurOutEndLine();	
 			
-			input = getCommand();			
+			if (mout->control_pressed) { input = "quit()"; }
 			
 			//allow user to omit the () on the quit command
 			if (input == "quit") { input = "quit()"; }
@@ -62,20 +67,32 @@ bool InteractEngine::getInput(){
 			options = parser.getOptionString();
 			
 			if (commandName != "") {
-			
+				mout->executing = true;
+				
+				#ifdef USE_MPI
+					int pid;
+					MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					
+					if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+				#endif
 				//executes valid command
 				Command* command = cFactory->getCommand(commandName, options);
 				quitCommandCalled = command->execute();
+				mout->control_pressed = 0;
+				mout->executing = false;
 				
+				#ifdef USE_MPI
+					}
+				#endif
 			}else {
-				mothurOut("Your input contains errors. Please try again."); 
-				mothurOutEndLine();
+				mout->mothurOut("Your input contains errors. Please try again."); 
+				mout->mothurOutEndLine();
 			}
 		}	
 		return 1;
 	}
 	catch(exception& e) {
-		errorOut(e, "InteractEngine", "getInput");
+		mout->errorOut(e, "InteractEngine", "getInput");
 		exit(1);
 	}
 }
@@ -86,27 +103,37 @@ string Engine::getCommand()  {
 			#ifdef USE_READLINE
 				char* nextCommand = NULL;
 				nextCommand = readline("mothur > ");
-				if(nextCommand != NULL) {  add_history(nextCommand);  }		
-				mothurOutJustToLog("mothur > " + toString(nextCommand));
+				
+				if(nextCommand != NULL) {  add_history(nextCommand);  }	
+				else{ //^D causes null string and we want it to quit mothur
+					nextCommand = "quit"; 
+					mout->mothurOut(nextCommand);
+				}	
+				
+				mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
 				return nextCommand;
 			#else
 				string nextCommand = "";
-				mothurOut("mothur > ");
+				mout->mothurOut("mothur > ");
 				getline(cin, nextCommand);
+				mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+				
 				return nextCommand;
 			#endif
 		#else
-			string nextCommand = "";
-			mothurOut("mothur > ");
-			getline(cin, nextCommand);
-			return nextCommand;
+				string nextCommand = "";
+				
+				mout->mothurOut("mothur > ");
+				getline(cin, nextCommand);
+				mout->mothurOutJustToLog(toString(nextCommand));
+				
+				return nextCommand;
 		#endif
-		
-		mothurOutEndLine();
+	
 						
 	}
 	catch(exception& e) {
-		errorOut(e, "Engine", "getCommand");
+		mout->errorOut(e, "Engine", "getCommand");
 		exit(1);
 	}
 }
@@ -121,7 +148,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 				
 	}
 	catch(exception& e) {
-		errorOut(e, "BatchEngine", "BatchEngine");
+		mout->errorOut(e, "BatchEngine", "BatchEngine");
 		exit(1);
 	}
 }
@@ -136,8 +163,8 @@ bool BatchEngine::getInput(){
 	try {
 		//check if this is a valid batchfile
 		if (openedBatch == 1) {  
-			mothurOut("unable to open batchfile");  
-			mothurOutEndLine();
+			mout->mothurOut("unable to open batchfile");  
+			mout->mothurOutEndLine();
 			return 1; 
 		}
 	
@@ -155,10 +182,11 @@ bool BatchEngine::getInput(){
 			
 			if (input[0] != '#') {
 				
-				mothurOutEndLine();
-				mothurOut("mothur > " + input);
-				mothurOutEndLine();
-				
+				mout->mothurOutEndLine();
+				mout->mothurOut("mothur > " + input);
+				mout->mothurOutEndLine();
+							
+				if (mout->control_pressed) { input = "quit()"; }
 				
 				//allow user to omit the () on the quit command
 				if (input == "quit") { input = "quit()"; }
@@ -168,13 +196,25 @@ bool BatchEngine::getInput(){
 				options = parser.getOptionString();
 										
 				if (commandName != "") {
-
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid;
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+					#endif
 					//executes valid command
 					Command* command = cFactory->getCommand(commandName, options);
 					quitCommandCalled = command->execute();
+					mout->control_pressed = 0;
+					mout->executing = false;
+				
+					#ifdef USE_MPI
+						}
+					#endif
 				}else {		
-					mothurOut("Invalid."); 
-					mothurOutEndLine();
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
 				}
 				
 			}
@@ -185,7 +225,7 @@ bool BatchEngine::getInput(){
 		return 1;
 	}
 	catch(exception& e) {
-		errorOut(e, "BatchEngine", "getInput");
+		mout->errorOut(e, "BatchEngine", "getInput");
 		exit(1);
 	}
 }
@@ -202,10 +242,10 @@ ScriptEngine::ScriptEngine(string path, string commandString){
 		listOfCommands = commandString.substr(1, (commandString.length()-1));
 
 		globaldata->argv = path;
-		
+				
 	}
 	catch(exception& e) {
-		errorOut(e, "ScriptEngine", "ScriptEngine");
+		mout->errorOut(e, "ScriptEngine", "ScriptEngine");
 		exit(1);
 	}
 }
@@ -233,11 +273,11 @@ bool ScriptEngine::getInput(){
 			
 			if (input == "") { input = "quit()"; }
 			
+			mout->mothurOutEndLine();
+			mout->mothurOut("mothur > " + input);
+			mout->mothurOutEndLine();
 			
-			mothurOutEndLine();
-			mothurOut("mothur > " + input);
-			mothurOutEndLine();
-
+			if (mout->control_pressed) { input = "quit()"; }
 				
 			//allow user to omit the () on the quit command
 			if (input == "quit") { input = "quit()"; }
@@ -247,13 +287,25 @@ bool ScriptEngine::getInput(){
 			options = parser.getOptionString();
 										
 			if (commandName != "") {
-
+				mout->executing = true;
+				#ifdef USE_MPI
+					int pid;
+					MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					
+					if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+				#endif
 				//executes valid command
 				Command* command = cFactory->getCommand(commandName, options);
 				quitCommandCalled = command->execute();
+				mout->control_pressed = 0;
+				mout->executing = false;
+				
+				#ifdef USE_MPI
+					}
+				#endif
 			}else {		
-				mothurOut("Invalid."); 
-				mothurOutEndLine();
+				mout->mothurOut("Invalid."); 
+				mout->mothurOutEndLine();
 			}
 			
 		}
@@ -261,7 +313,7 @@ bool ScriptEngine::getInput(){
 		return 1;
 	}
 	catch(exception& e) {
-		errorOut(e, "ScriptEngine", "getInput");
+		mout->errorOut(e, "ScriptEngine", "getInput");
 		exit(1);
 	}
 }
@@ -296,7 +348,7 @@ string ScriptEngine::getNextCommand(string& commandString) {
 		return nextcommand;
 	}
 	catch(exception& e) {
-		errorOut(e, "ScriptEngine", "getNextCommand");
+		mout->errorOut(e, "ScriptEngine", "getNextCommand");
 		exit(1);
 	}
 }