X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=engine.cpp;h=e4e107168c5723c82b90a7f103ccb8d9ee83cb60;hp=42938d8a0bf157e0d31a837134d477bc65dca9c3;hb=615301e57c25e241356a9c2380648d117709458d;hpb=0bb069a445785a88a95e3f1427afba7df056a0b3

diff --git a/engine.cpp b/engine.cpp
index 42938d8..e4e1071 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -14,20 +14,35 @@
 
 #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;
 	
+	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;
 }
 
 /***********************************************************************/
 
-InteractEngine::~InteractEngine(){
-	}
+InteractEngine::~InteractEngine(){}
 
 /***********************************************************************/
 //This function allows the user to input commands one line at a time until they quit.
@@ -39,72 +54,171 @@ bool InteractEngine::getInput(){
 		string options = "";
 		int 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
+                    
+			if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'.  I changed them to '_' to avoid problems in your downstream analysis.\n"); }
+                    
+			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()"; }
+
 			
+			#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
-				CommandFactory cFactory;
-				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->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.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);
 	}
 }
-
 /***********************************************************************/
-//This function opens the batchfile to be used by BatchEngine::getInput.
-BatchEngine::BatchEngine(string path, string batchFileName){
+string Engine::getCommand()  {
 	try {
-		globaldata = GlobalData::getInstance();
 	
-		openedBatch = openInputFile(batchFileName, inputBatchFile);
-		globaldata->argv = path;
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+			#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 = strdup("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) {
+		mout->errorOut(e, "Engine", "getCommand");
+		exit(1);
+	}
+}
+/***********************************************************************/
+//This function opens the batchfile to be used by BatchEngine::getInput.
+BatchEngine::BatchEngine(string path, string batchFileName){
+	try {
 	
-	//	char buffer = ' ';
-	//	ifstream header("introtext.txt");
-	//	while(!header.eof()){
-	//		cout << buffer;
-	//		buffer = header.get();
-	//	}
+		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);
 	}
 }
 
 /***********************************************************************/
 
-BatchEngine::~BatchEngine(){
-	}
+BatchEngine::~BatchEngine(){	}
 
 /***********************************************************************/
 //This Function allows the user to run a batchfile containing several commands on Dotur
@@ -112,8 +226,8 @@ 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; 
 		}
 	
@@ -123,20 +237,54 @@ bool BatchEngine::getInput(){
 		
 		//CommandFactory cFactory;
 		int quitCommandCalled = 0;
+	    int count = 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(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);
 	
-		while(quitCommandCalled == 0){
-	
-			if (inputBatchFile.eof()) { input = "quit()"; }
-			else { getline(inputBatchFile, input); }
+					}
+				}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] != '#') {
-				
-				mothurOutEndLine();
-				mothurOut("mothur > " + input);
-				mothurOutEndLine();
-				
+				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()"; }
@@ -146,55 +294,100 @@ 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
-					CommandFactory cFactory;
-					Command* command = cFactory.getCommand(commandName, options);
-					quitCommandCalled = command->execute();
+                    mout->changedSeqNames = false;
+					mout->runParse = true;
+					mout->clearGroups();
+					mout->clearAllGroups();
+					mout->Treenames.clear();
+					mout->saveNextLabel = "";
+					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.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 {		
-					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));
-
-		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;
+				
 	}
 	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
@@ -209,17 +402,57 @@ 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()"; }
@@ -229,36 +462,83 @@ 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->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.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
-				CommandFactory cFactory;
-				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;
 		
-		nextcommand = commandString.substr(0,commandString.find_first_of(';'));
-
+		//go through string until you reach ; or end
+		while (count < commandString.length()) { 
+			
+			 //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++;
+		}
+		
+		//if you are not at the end
+		if (count != commandString.length())  {   commandString = commandString.substr(count+1, commandString.length());  }
+		else { commandString = ""; }
 				
-		if ((commandString.find_first_of(';')+1) <= commandString.length()) {
-			commandString = commandString.substr(commandString.find_first_of(';')+1, commandString.length());
-		}else { commandString = ""; } //you have reached the last command.
 		
 		//get rid of spaces in between commands if any
 		if (commandString.length() > 0) {
@@ -267,11 +547,11 @@ 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);
 	}
 }