X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=engine.cpp;h=d6be4e4f1a16e00af29cfe36052c98e3a6e98efb;hp=593c2c3128d08cfe8abddfa81a1e384a1d17aa62;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=c82900be3ceed3d9bc491bdc98b1819ef85c1af7

diff --git a/engine.cpp b/engine.cpp
index 593c2c3..d6be4e4 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -18,19 +18,26 @@
 Engine::Engine(){
 	try {
 		cFactory = CommandFactory::getInstance();
+		mout = MothurOut::getInstance();
 	}
 	catch(exception& e) {
-		errorOut(e, "Engine", "Engine");
+		mout->errorOut(e, "Engine", "Engine");
 		exit(1);
 	}
 }
+/***********************************************************************/
 
 /***********************************************************************/
 
 InteractEngine::InteractEngine(string path){
 
-	globaldata = GlobalData::getInstance();
-	globaldata->argv = path;
+	
+	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 = mout->findProgramPath("mothur"); }
+	
+	mout->argv = path;
 }
 
 /***********************************************************************/
@@ -49,64 +56,144 @@ bool InteractEngine::getInput(){
 		
 		while(quitCommandCalled != 1){
 
-			mothurOutEndLine();
+			#ifdef USE_MPI
+				int pid, processors;
+				MPI_Status status;
+				MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+				MPI_Comm_size(MPI_COMM_WORLD, &processors);
+				
+				if (pid == 0) {
+				
+			#endif
+                    
+			if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n"); }
+                    
+			mout->mothurOutEndLine();
 			
-			input = getCommand();			
+			input = getCommand();	
+			mout->mothurOutEndLine();	
+			
+			if (mout->control_pressed) { input = "quit()"; }
 			
 			//allow user to omit the () on the quit command
 			if (input == "quit") { input = "quit()"; }
+
+			
+			#ifdef USE_MPI
+				//send commandName
+				for(int i = 1; i < processors; i++) { 
+						int length = input.length();
+						MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+						MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+	
+					}
+				}else {
+					int length;
+					MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+					//recieve container
+					char* tempBuf = new char[length];
+					MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+					
+					input = tempBuf;
+					if (input.length() > length) { input = input.substr(0, length);  }
+					delete tempBuf;	
+				}
+
 			
+			#endif
+		
 			CommandOptionParser parser(input);
 			commandName = parser.getCommandString();
 	
 			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 ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+					//cout << pid << " is in execute " << commandName << endl;
+					#endif
+					//executes valid command
+                    mout->changedSeqNames = false;
+					mout->runParse = true;
+					mout->clearGroups();
+					mout->clearAllGroups();
+					mout->Treenames.clear();
+					mout->saveNextLabel = "";
+                    mout->commandInputsConvertError = false;
+					mout->printedSharedHeaders = false;
+					mout->currentSharedBinLabels.clear();
+					mout->sharedBinLabelsInFile.clear();
+                    mout->printedListHeaders = false;
+                    mout->listBinLabelsInFile.clear();
+							
+					Command* command = cFactory->getCommand(commandName, options);
+					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(); }
+
+					mout->control_pressed = 0;
+					mout->executing = false;
+										
+					#ifdef USE_MPI
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					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)
+	
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			#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 = strdup("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);
 	}
 }
@@ -114,14 +201,19 @@ 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 = openInputFile(batchFileName, inputBatchFile);
-		globaldata->argv = path;
+		openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
+		
+		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 = mout->findProgramPath("mothur"); }
+		
+		mout->argv = path;
 				
 	}
 	catch(exception& e) {
-		errorOut(e, "BatchEngine", "BatchEngine");
+		mout->errorOut(e, "BatchEngine", "BatchEngine");
 		exit(1);
 	}
 }
@@ -136,8 +228,8 @@ 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; 
 		}
 	
@@ -147,18 +239,54 @@ bool BatchEngine::getInput(){
 		
 		//CommandFactory cFactory;
 		int quitCommandCalled = 0;
-	
-		while(quitCommandCalled == 0){
-	
-			if (inputBatchFile.eof()) { input = "quit()"; }
-			else { input = getline(inputBatchFile); }
+	    int count = 0;
+		while(quitCommandCalled != 1){
 			
-			if (input[0] != '#') {
+			#ifdef USE_MPI
+				int pid, processors;
+				MPI_Status status;
+				MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+				MPI_Comm_size(MPI_COMM_WORLD, &processors);
 				
-				mothurOutEndLine();
-				mothurOut("mothur > " + input);
-				mothurOutEndLine();
+				if (pid == 0) {
 				
+			#endif
+			
+			input = getNextCommand(inputBatchFile);
+			count++;
+			
+			#ifdef USE_MPI
+				//send commandName
+				for(int i = 1; i < processors; i++) { 
+						int length = input.length();
+						MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+						MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+	
+					}
+				}else {
+					int length;
+					MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+					//recieve container
+					char* tempBuf = new char[length];
+					MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+					
+					input = tempBuf;
+					if (input.length() > length) { input = input.substr(0, length);  }
+					delete tempBuf;	
+				}
+
+			
+			#endif
+
+			
+			
+			if (input[0] != '#') {
+				if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n"); }
+				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()"; }
@@ -168,44 +296,95 @@ bool BatchEngine::getInput(){
 				options = parser.getOptionString();
 										
 				if (commandName != "") {
-
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid;
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						
+//cout << pid << " is here " << commandName << '\t' << count << endl;
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+					#endif
 					//executes valid command
+                    mout->changedSeqNames = false;
+					mout->runParse = true;
+					mout->clearGroups();
+					mout->clearAllGroups();
+					mout->Treenames.clear();
+					mout->saveNextLabel = "";
+					mout->commandInputsConvertError = false;
+                    mout->printedSharedHeaders = false;
+                    mout->currentSharedBinLabels.clear();
+                    mout->sharedBinLabelsInFile.clear();
+                    mout->printedListHeaders = false;
+                    mout->listBinLabelsInFile.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(); }
+
+					mout->control_pressed = 0;
+					mout->executing = false;
+										
+					#ifdef USE_MPI
+						}
+					#endif
 				}else {		
-					mothurOut("Invalid."); 
-					mothurOutEndLine();
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
 				}
 				
 			}
-			gobble(inputBatchFile);
+			mout->gobble(inputBatchFile);
 		}
 		
 		inputBatchFile.close();
 		return 1;
 	}
 	catch(exception& e) {
-		errorOut(e, "BatchEngine", "getInput");
+		mout->errorOut(e, "BatchEngine", "getInput");
+		exit(1);
+	}
+}
+/***********************************************************************/
+string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
+	try {
+			
+		string nextcommand = "";
+		
+		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
+		else { nextcommand = mout->getline(inputBatchFile); }
+		
+		return nextcommand;
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "BatchEngine", "getNextCommand");
 		exit(1);
 	}
 }
-
 
 /***********************************************************************/
 /***********************************************************************/
 //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));
+		
+		string temppath = path.substr(0, (path.find_last_of("othur")-5));
 
-		globaldata->argv = path;
+		//this will happen if you set the path variable to contain mothur's exe location
+		if (temppath == "") { path = mout->findProgramPath("mothur"); }
 		
+		mout->argv = path;
+				
 	}
 	catch(exception& e) {
-		errorOut(e, "ScriptEngine", "ScriptEngine");
+		mout->errorOut(e, "ScriptEngine", "ScriptEngine");
 		exit(1);
 	}
 }
@@ -227,17 +406,57 @@ bool ScriptEngine::getInput(){
 		//CommandFactory cFactory;
 		int quitCommandCalled = 0;
 	
-		while(quitCommandCalled == 0){
-		
+		while(quitCommandCalled != 1){
+			
+			#ifdef USE_MPI
+				int pid, processors;
+				MPI_Status status;
+				MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+				MPI_Comm_size(MPI_COMM_WORLD, &processors);
+				
+				if (pid == 0) {
+				
+			#endif
+			
 			input = getNextCommand(listOfCommands);	
 			
 			if (input == "") { input = "quit()"; }
+                    
+            if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n"); }
 			
+			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();
+			}
 			
-			mothurOutEndLine();
-			mothurOut("mothur > " + input);
-			mothurOutEndLine();
+			#ifdef USE_MPI
+				//send commandName
+				for(int i = 1; i < processors; i++) { 
+						int length = input.length();
+						MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+						MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+	
+					}
+				}else {
+					int length;
+					MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+					//recieve container
+					char* tempBuf = new char[length];
+					MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+					
+					input = tempBuf;
+					if (input.length() > length) { input = input.substr(0, length);  }
+					delete tempBuf;	
+				}
 
+			
+			#endif
+			
+			
+			if (mout->control_pressed) { input = "quit()"; }
 				
 			//allow user to omit the () on the quit command
 			if (input == "quit") { input = "quit()"; }
@@ -247,34 +466,76 @@ bool ScriptEngine::getInput(){
 			options = parser.getOptionString();
 										
 			if (commandName != "") {
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid, numProcesses;
+						
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						MPI_Comm_size(MPI_COMM_WORLD, &numProcesses); 
+					
+//cout << pid << " is here " << commandName  << endl;
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+							//cout << pid << " is in execute" << endl;	
+					#endif
+					//executes valid command
+                    mout->changedSeqNames = false;
+					mout->runParse = true;
+					mout->clearGroups();
+					mout->clearAllGroups();
+					mout->Treenames.clear();
+					mout->saveNextLabel = "";
+                    mout->commandInputsConvertError = false;
+                    mout->printedSharedHeaders = false;
+                    mout->currentSharedBinLabels.clear();
+                    mout->sharedBinLabelsInFile.clear();
+                    mout->printedListHeaders = false;
+                    mout->listBinLabelsInFile.clear();
+
+					Command* command = cFactory->getCommand(commandName, options);
+					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(); }
+							
+					mout->control_pressed = 0;
+					mout->executing = false;
+									
+					#ifdef USE_MPI
+					//cout << pid << " is done in execute" << 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 {
+		
 		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++;
@@ -292,11 +553,11 @@ 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);
 	}
 }