X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=engine.cpp;h=e4e107168c5723c82b90a7f103ccb8d9ee83cb60;hp=68a75005f1521411227b20fe9ed253ec0b902e1c;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d

diff --git a/engine.cpp b/engine.cpp
index 68a7500..e4e1071 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -10,29 +10,39 @@
  *  Fix later, don't have time now.
  *
  */
-using namespace std;
+
 
 #include "engine.hpp"
 
+/***********************************************************************/
+Engine::Engine(){
+	try {
+		cFactory = CommandFactory::getInstance();
+		mout = MothurOut::getInstance();
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "Engine", "Engine");
+		exit(1);
+	}
+}
 /***********************************************************************/
 
-InteractEngine::InteractEngine(){
+/***********************************************************************/
 
-	globaldata = GlobalData::getInstance();
+InteractEngine::InteractEngine(string path){
 
-	system("clear");
-//	char buffer = ' ';
-//	ifstream header("introtext.txt");
-//	while(!header.eof()){
-//		cout << buffer;
-//		buffer = header.get();
-//	}
+	
+	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.
@@ -41,136 +51,508 @@ bool InteractEngine::getInput(){
 	try {
 		string input = "";
 		string commandName = "";
+		string options = "";
 		int quitCommandCalled = 0;
-		bool errorFree;
-		ErrorCheck* errorCheckor = new ErrorCheck();
-		
-		cout << "mothur v1.0" << endl;
-		cout << "Last updated: 1/29/2009" << endl << endl;
-		cout << "by" << endl;
-		cout << "Patrick D. Schloss" << endl << endl;
-		cout << "Department of Microbiology" << endl;
-		cout << "The University of Massachusetts" << endl;
-		cout << "pschloss@micro.umass.edu" << endl;
-		cout << "http://schloss.micro.umass.edu/mothur" << endl << endl << endl;
-		cout << "Distributed under the GNU General Public License" << endl << endl;
-		cout << "Type 'help()' for information on the commands that are available" << endl << endl;
-		cout << "Type 'quit()' to exit program" << endl;
-
+		
 		while(quitCommandCalled != 1){
 
-			cout << endl << "mothur > ";
-			getline(cin, input);
-			if (cin.eof()) { input = "quit()"; }
+			#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();
 			
-			errorFree = errorCheckor->checkInput(input);
-			if (errorFree == true) {
-				CommandOptionParser parser(input);
-				commandName = parser.getCommandString();
+			input = getCommand();	
+			mout->mothurOutEndLine();	
+			
+			if (mout->control_pressed) { input = "quit()"; }
 			
-				//executes valid command
-				CommandFactory cFactory;
-				Command* command = cFactory.getCommand(commandName);
-				quitCommandCalled = command->execute();
+			//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
 		
-			}else {
-					cout << "Your input contains errors. Please try again." << endl;
-			}
+			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)) {
+					//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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the InteractEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		mout->errorOut(e, "InteractEngine", "getInput");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the InteractEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/***********************************************************************/
+string Engine::getCommand()  {
+	try {
+	
+		#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 batchFileName){
+BatchEngine::BatchEngine(string path, string batchFileName){
 	try {
-		globaldata = GlobalData::getInstance();
-		openedBatch = openInputFile(batchFileName, inputBatchFile);
-
-		system("clear");
 	
-	//	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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the BatchEngine class function BatchEngine. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		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
 bool BatchEngine::getInput(){
 	try {
+		//check if this is a valid batchfile
+		if (openedBatch == 1) {  
+			mout->mothurOut("unable to open batchfile");  
+			mout->mothurOutEndLine();
+			return 1; 
+		}
+	
 		string input = "";
 		string commandName = "";
-		bool errorFree;
-		ErrorCheck* errorCheckor = new ErrorCheck();
-
-		CommandFactory cFactory;
+		string options = "";
+		
+		//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){
-		
-			getline(inputBatchFile, input);
-			if (inputBatchFile.eof()) { input = "quit()"; }
+					}
+				}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
+
 			
-			cout << endl << "mothur > " << input << endl;
-			errorFree = errorCheckor->checkInput(input);
-			if (errorFree == true) {
+			
+			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()"; }
+
 				CommandOptionParser parser(input);
 				commandName = parser.getCommandString();
-				ifstream filehandle;
-		
-				if (openedBatch == 0) { //able to open batchfile
+				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);
-					quitCommandCalled = command->execute();
-				}
-				else {
-					cout << "Invalid." << endl;
+                    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();
 				}
+				
 			}
-			else {
-				cout << "Unable to open batchfile." << endl;
-			}
+			mout->gobble(inputBatchFile);
 		}
+		
+		inputBatchFile.close();
 		return 1;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the BatchEngine class Function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		mout->errorOut(e, "BatchEngine", "getInput");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the BatchEngine class function getInput. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/***********************************************************************/
+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 {
+		
+		//remove quotes
+		listOfCommands = commandString.substr(1, (commandString.length()-1));
+		
+		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) {
+		mout->errorOut(e, "ScriptEngine", "ScriptEngine");
 		exit(1);
 	}
 }
 
+/***********************************************************************/
+
+ScriptEngine::~ScriptEngine(){ 	}
 
 /***********************************************************************/
+//This Function allows the user to run a batchfile containing several commands on mothur
+bool ScriptEngine::getInput(){
+	try {
+			
+		string input = "";
+		string commandName = "";
+		string options = "";
+		
+		
+		//CommandFactory cFactory;
+		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
+			
+			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();
+			}
+			
+			#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()"; }
+
+			CommandOptionParser parser(input);
+			commandName = parser.getCommandString();
+			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();
+				}
+
+			
+		}
+		
+		return 1;
+	}
+	catch(exception& e) {
+		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()) { 
+			
+			 //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 = ""; }
+				
+		
+		//get rid of spaces in between commands if any
+		if (commandString.length() > 0) {
+			while (commandString[0] == ' ') {  
+				commandString = commandString.substr(1,commandString.length());
+				if (commandString.length() == 0) {  break;  }
+			}
+		}
+		
+		return nextcommand;
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "ScriptEngine", "getNextCommand");
+		exit(1);
+	}
+}
+/***********************************************************************/