X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=c6ceb59d051d6fb88fe1e169bdd9206da9d58ef8;hb=438aa88dbc092d9c1c80ec3fa20c8e47f97101c4;hp=e5898036e2e4ebd5ddea0af89735ed7efacdf924;hpb=1d58557e4ce9f1b2d54db61937c161d889d6558b;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index e589803..c6ceb59 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -14,6 +14,18 @@
 
 #include "engine.hpp"
 
+/***********************************************************************/
+Engine::Engine(){
+	try {
+		cFactory = CommandFactory::getInstance();
+		mout = MothurOut::getInstance();
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "Engine", "Engine");
+		exit(1);
+	}
+}
+
 /***********************************************************************/
 
 InteractEngine::InteractEngine(string path){
@@ -21,13 +33,11 @@ InteractEngine::InteractEngine(string path){
 	globaldata = GlobalData::getInstance();
 	globaldata->argv = path;
 	
-	
 }
 
 /***********************************************************************/
 
-InteractEngine::~InteractEngine(){
-	}
+InteractEngine::~InteractEngine(){}
 
 /***********************************************************************/
 //This function allows the user to input commands one line at a time until they quit.
@@ -39,44 +49,95 @@ bool InteractEngine::getInput(){
 		string options = "";
 		int quitCommandCalled = 0;
 		
-				
 		while(quitCommandCalled != 1){
+
+			mout->mothurOutEndLine();
 			
-			mothurOutEndLine();
-			mothurOut("mothur > ");
-			getline(cin, input);
-			if (cin.eof()) { input = "quit()"; }
+			input = getCommand();	
+			mout->mothurOutEndLine();	
 			
-			mothurOutJustToLog(input);
-			mothurOutEndLine();
+			if (mout->control_pressed) { input = "quit()"; }
 			
 			//allow user to omit the () on the quit command
 			if (input == "quit") { input = "quit()"; }
 			
 			CommandOptionParser parser(input);
 			commandName = parser.getCommandString();
+	
 			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
-				CommandFactory cFactory;
-				Command* command = cFactory.getCommand(commandName, options);
+				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);
+	}
+}
+/***********************************************************************/
+string Engine::getCommand()  {
+	try {
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#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
+					nextCommand = "quit"; 
+					mout->mothurOut(nextCommand);
+				}	
+				
+				mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+				return nextCommand;
+			#else
+				string nextCommand = "";
+				mout->mothurOut("mothur > ");
+				getline(cin, nextCommand);
+				mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+				
+				return nextCommand;
+			#endif
+		#else
+				string nextCommand = "";
+				
+				mout->mothurOut("mothur > ");
+				getline(cin, nextCommand);
+				mout->mothurOutJustToLog(toString(nextCommand));
+				
+				return nextCommand;
+		#endif
+		
+		mout->mothurOutEndLine();
+						
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "Engine", "getCommand");
 		exit(1);
 	}
 }
-
 /***********************************************************************/
 //This function opens the batchfile to be used by BatchEngine::getInput.
 BatchEngine::BatchEngine(string path, string batchFileName){
@@ -88,15 +149,14 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 				
 	}
 	catch(exception& e) {
-		errorOut(e, "BatchEngine", "BatchEngine");
+		mout->errorOut(e, "BatchEngine", "BatchEngine");
 		exit(1);
 	}
 }
 
 /***********************************************************************/
 
-BatchEngine::~BatchEngine(){
-	}
+BatchEngine::~BatchEngine(){	}
 
 /***********************************************************************/
 //This Function allows the user to run a batchfile containing several commands on Dotur
@@ -104,8 +164,8 @@ 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; 
 		}
 	
@@ -119,17 +179,15 @@ bool BatchEngine::getInput(){
 		while(quitCommandCalled == 0){
 	
 			if (inputBatchFile.eof()) { input = "quit()"; }
-			else { getline(inputBatchFile, input); }
-	//cout << "input = ";		
-	//for (int i = 0; i < input.size();  i++) {  cout << input[i];  if ((input[i] == '\n') || (input[i] == '\r')) {  char c = input[i]; cout << "line feed = " << c << endl; } }
-	//cout << endl;		
+			else { input = getline(inputBatchFile); }
 			
 			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()"; }
@@ -139,14 +197,25 @@ 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
-					CommandFactory cFactory;
-					Command* command = cFactory.getCommand(commandName, options);
+					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();
 				}
 				
 			}
@@ -157,7 +226,7 @@ bool BatchEngine::getInput(){
 		return 1;
 	}
 	catch(exception& e) {
-		errorOut(e, "BatchEngine", "getInput");
+		mout->errorOut(e, "BatchEngine", "getInput");
 		exit(1);
 	}
 }
@@ -174,20 +243,17 @@ 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);
 	}
 }
 
 /***********************************************************************/
 
-ScriptEngine::~ScriptEngine(){
-	}
+ScriptEngine::~ScriptEngine(){ 	}
 
 /***********************************************************************/
 //This Function allows the user to run a batchfile containing several commands on mothur
@@ -208,11 +274,11 @@ 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()"; }
@@ -222,14 +288,25 @@ 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
-				CommandFactory cFactory;
-				Command* command = cFactory.getCommand(commandName, options);
+				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();
 			}
 			
 		}
@@ -237,7 +314,7 @@ bool ScriptEngine::getInput(){
 		return 1;
 	}
 	catch(exception& e) {
-		errorOut(e, "ScriptEngine", "getInput");
+		mout->errorOut(e, "ScriptEngine", "getInput");
 		exit(1);
 	}
 }
@@ -272,7 +349,7 @@ string ScriptEngine::getNextCommand(string& commandString) {
 		return nextcommand;
 	}
 	catch(exception& e) {
-		errorOut(e, "ScriptEngine", "getNextCommand");
+		mout->errorOut(e, "ScriptEngine", "getNextCommand");
 		exit(1);
 	}
 }