X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=engine.cpp;h=e4e107168c5723c82b90a7f103ccb8d9ee83cb60;hp=acd417cd8477516f2a670f6a34257964d6c442c3;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=1f78a8c454a636f19b4711bd52782ea1e3e81d3d

diff --git a/engine.cpp b/engine.cpp
index acd417c..e4e1071 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -25,14 +25,19 @@ 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;
 }
 
 /***********************************************************************/
@@ -51,6 +56,18 @@ bool InteractEngine::getInput(){
 		
 		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();
 			
 			input = getCommand();	
@@ -60,7 +77,31 @@ bool InteractEngine::getInput(){
 			
 			//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();
 	
@@ -72,29 +113,32 @@ bool InteractEngine::getInput(){
 						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)) {
+					//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);
-					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
-							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 {		
@@ -112,14 +156,15 @@ cout << pid << " is here " << commandName << endl;
 /***********************************************************************/
 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);  }	
 				else{ //^D causes null string and we want it to quit mothur
-					nextCommand = "quit"; 
+					nextCommand = strdup("quit");
 					mout->mothurOut(nextCommand);
 				}	
 				
@@ -154,10 +199,15 @@ 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) {
@@ -187,14 +237,49 @@ 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 { input = getline(inputBatchFile); }
+					}
+				}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();
@@ -214,29 +299,33 @@ bool BatchEngine::getInput(){
 						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;
+//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->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.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
-							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 {		
@@ -245,7 +334,7 @@ cout << pid << " is here " << commandName << endl;
 				}
 				
 			}
-			gobble(inputBatchFile);
+			mout->gobble(inputBatchFile);
 		}
 		
 		inputBatchFile.close();
@@ -256,19 +345,38 @@ cout << pid << " is here " << commandName << endl;
 		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) {
@@ -294,15 +402,55 @@ 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();
+			}
+			
+			#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
 			
-			mout->mothurOutEndLine();
-			mout->mothurOut("mothur > " + input);
-			mout->mothurOutEndLine();
 			
 			if (mout->control_pressed) { input = "quit()"; }
 				
@@ -317,45 +465,38 @@ bool ScriptEngine::getInput(){
 					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;
+//cout << pid << " is here " << commandName  << endl;
 						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
-							cout << pid << " is in execute" << endl;	
+							//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);
-					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
-					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;
-							}
+					//cout << pid << " is done in execute" << endl;
 						}
 					#endif
 				}else {		
@@ -377,18 +518,18 @@ cout << pid << " is here " << commandName  << endl;
 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;
+		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++;