X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=acd417cd8477516f2a670f6a34257964d6c442c3;hb=1f78a8c454a636f19b4711bd52782ea1e3e81d3d;hp=371bda8fb83f2b8ceb4793c49f067ed5987f2094;hpb=648ec37228eb16075ace911dd5a5773cdfe683da;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index 371bda8..acd417c 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -14,12 +14,25 @@
 
 #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){
 
 	globaldata = GlobalData::getInstance();
 	globaldata->argv = path;
+	
 }
 
 /***********************************************************************/
@@ -36,89 +49,104 @@ bool InteractEngine::getInput(){
 		string options = "";
 		int quitCommandCalled = 0;
 		
-				
 		while(quitCommandCalled != 1){
+
+			mout->mothurOutEndLine();
 			
-			mothurOutEndLine();
-			mothurOut("mothur > ");
-			
-			//get input char by char so you can check for use of arrow keys
-			//if (_kbhit()){
-			//	_getch(); // edit : if you want to check the arrow-keys you must call getch twice because special-keys have two values
-			//	return _getch();
-			//}
-			//return 0; // if no key is pressed
-			//setbuf(stdin, NULL); //no buffering
-/*if(ch==0)
-{
-ch=getch();
-if(ch==72) cout<<"up";
-else if(ch==75) cout<<"left";
-else if(ch==77) cout<<"right";
-else if(ch==80) cout<<"down";
-cout<<endl;
-}
-else break;
-}
-delay(2000);
-return 0;
-}*/
-			
-			//int letter = 0;
-			//while ((letter != 10) && (letter != 13)) {
-			//	letter = getch();
-				
-			//	cout << "char code = " << letter << endl;
-				
-			//	input += char(letter);
-			//}
-		//	input = input.substr(0, input.length()-1); //cut off newline char
-		
-	//cout << input << endl;		
-			
-			getline(cin, input);
-			if (cin.eof()) { input = "quit()"; }
-			
-			//save command
-			//previousInputs.push_back(input);
+			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();
-	//cout << " command = " << commandName << endl;
+	
 			options = parser.getOptionString();
 			
 			if (commandName != "") {
-			
-				//executes valid command
-				Command* command = cFactory->getCommand(commandName, options);
-				quitCommandCalled = command->execute();
-				
-			}else {
-				mothurOut("Your input contains errors. Please try again."); 
-				mothurOutEndLine();
-			}
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid;
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						
+						if ((pid != 0) && !(cFactory->MPIEnabled(commandName))) {
+cout << pid << " is waiting " << commandName << endl;						
+							char buf[4];
+							MPI_Bcast(buf, 4, MPI_CHAR, 0, MPI_COMM_WORLD); //make everyone wait - just in case
+						}
+ 
+cout << pid << " is here " << commandName << endl;
+						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
+							if (!(cFactory->MPIEnabled(commandName))) {
+								char buf[4];
+								strcpy(buf, "done"); 
+
+								MPI_Bcast(buf, 4, MPI_CHAR, 0, MPI_COMM_WORLD); //make everyone wait - just in case
+				cout << pid << " is broadcasting " << endl;
+							}
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
+				}
 		}	
 		return 1;
 	}
 	catch(exception& e) {
-		errorOut(e, "InteractEngine", "getInput");
+		mout->errorOut(e, "InteractEngine", "getInput");
 		exit(1);
 	}
 }
 /***********************************************************************/
-void Engine::terminateCommand(int dummy)  {
+string Engine::getCommand()  {
 	try {
-		mothurOut("Stopping command."); mothurOutEndLine();
-		cFactory->getCommand();  //terminates command
+		#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
+	
+						
 	}
 	catch(exception& e) {
-		errorOut(e, "InteractEngine", "terminateCommand");
+		mout->errorOut(e, "Engine", "getCommand");
 		exit(1);
 	}
 }
@@ -133,7 +161,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 				
 	}
 	catch(exception& e) {
-		errorOut(e, "BatchEngine", "BatchEngine");
+		mout->errorOut(e, "BatchEngine", "BatchEngine");
 		exit(1);
 	}
 }
@@ -148,8 +176,8 @@ 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; 
 		}
 	
@@ -167,10 +195,11 @@ 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()"; }
@@ -180,13 +209,39 @@ bool BatchEngine::getInput(){
 				options = parser.getOptionString();
 										
 				if (commandName != "") {
-
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid;
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						
+						if ((pid != 0) && !(cFactory->MPIEnabled(commandName))) {
+cout << pid << " is waiting " << commandName << endl;						
+							char buf[4];
+							MPI_Bcast(buf, 4, MPI_CHAR, 0, MPI_COMM_WORLD); //make everyone wait - just in case
+						}
+ 
+cout << pid << " is here " << commandName << endl;
+						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
+							if (!(cFactory->MPIEnabled(commandName))) {
+								char buf[4];
+								strcpy(buf, "done"); 
+
+								MPI_Bcast(buf, 4, MPI_CHAR, 0, MPI_COMM_WORLD); //make everyone wait - just in case
+				cout << pid << " is broadcasting " << endl;
+							}
+						}
+					#endif
 				}else {		
-					mothurOut("Invalid."); 
-					mothurOutEndLine();
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
 				}
 				
 			}
@@ -197,7 +252,7 @@ bool BatchEngine::getInput(){
 		return 1;
 	}
 	catch(exception& e) {
-		errorOut(e, "BatchEngine", "getInput");
+		mout->errorOut(e, "BatchEngine", "getInput");
 		exit(1);
 	}
 }
@@ -214,10 +269,10 @@ 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);
 	}
 }
@@ -245,11 +300,11 @@ 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()"; }
@@ -259,27 +314,74 @@ bool ScriptEngine::getInput(){
 			options = parser.getOptionString();
 										
 			if (commandName != "") {
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid, numProcesses;
+						MPI_Status status; 
+						//MPI_Request request;
+						
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						MPI_Comm_size(MPI_COMM_WORLD, &numProcesses); 
+						
+						if ((pid != 0) && (!(cFactory->MPIEnabled(commandName)))) {
+cout << pid << " is waiting " << commandName << endl;						
+							char buf[12];
+							
+							MPI_Recv(buf, 12, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);  //make everyone wait - just in case
+							//MPI_Wait(&request, &status);
+					cout << pid << " received " << buf << endl;
+						}
+						
+					
+cout << pid << " is here " << commandName  << endl;
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+							cout << pid << " is in execute" << endl;	
+					#endif
+					//executes valid command
+					Command* command = cFactory->getCommand(commandName, options);
+					quitCommandCalled = command->execute();
+					mout->control_pressed = 0;
+					mout->executing = false;
+									
+					#ifdef USE_MPI
+					cout << pid << " is done in execute" << endl;
+							if ((pid == 0) && (!(cFactory->MPIEnabled(commandName)))) {
+								char buf[12];
+								strcpy(buf, "command done"); 
+								
+								for(int i = 1; i < numProcesses; i++) { 
+									MPI_Send(buf, 12, MPI_CHAR, i, 2001, MPI_COMM_WORLD); //make everyone wait - just in case
+									//MPI_Wait(&request, &status);
+						cout << pid << " sent " << buf << endl;
+								}
+				cout << pid << " is sending " << endl;
+							}
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
+				}
 
-				//executes valid command
-				Command* command = cFactory->getCommand(commandName, options);
-				quitCommandCalled = command->execute();
-			}else {		
-				mothurOut("Invalid."); 
-				mothurOutEndLine();
-			}
 			
 		}
 		
 		return 1;
 	}
 	catch(exception& e) {
-		errorOut(e, "ScriptEngine", "getInput");
+		mout->errorOut(e, "ScriptEngine", "getInput");
 		exit(1);
 	}
 }
 /***********************************************************************/
 string ScriptEngine::getNextCommand(string& commandString) {
 	try {
+		
+		#ifdef USE_MPI
+		int ierr = MPI_Barrier(MPI_COMM_WORLD);
+cout << "barrier = " << ierr << endl;
+		#endif
+		
 		string nextcommand = "";
 		int count = 0;
 		
@@ -304,11 +406,11 @@ string ScriptEngine::getNextCommand(string& commandString) {
 				if (commandString.length() == 0) {  break;  }
 			}
 		}
-					
+		
 		return nextcommand;
 	}
 	catch(exception& e) {
-		errorOut(e, "ScriptEngine", "getNextCommand");
+		mout->errorOut(e, "ScriptEngine", "getNextCommand");
 		exit(1);
 	}
 }