X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=54197174e1fa3da14861614734b1dc58314a466a;hb=7c08fa69c0b89e7a08341af2aa724f206f182075;hp=fbf986dc6965de7d9d269c31f35e99ed85467a9d;hpb=11c115c802602be50e106aae56969e15d2c49a62;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index fbf986d..5419717 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -25,19 +25,12 @@ Engine::Engine(){
 		exit(1);
 	}
 }
-
 /***********************************************************************/
-
-InteractEngine::InteractEngine(string path){
-
-	globaldata = GlobalData::getInstance();
-	
-	string temppath = path.substr(0, (path.find_last_of('m')));
-	
-	//this will happen if you set the path variable to contain mothur's exe location
-	if (temppath == "") { 
-	
+string Engine::findMothursPath(){
+	try { 
+		
 		string envPath = getenv("PATH");
+		string mothurPath = "";
 		
 		//delimiting path char
 		char delim;
@@ -49,10 +42,9 @@ InteractEngine::InteractEngine(string path){
 		
 		//break apart path variable by ':'
 		vector<string> dirs;
-		splitAtChar(envPath, dirs, delim);
+		mout->splitAtChar(envPath, dirs, delim);
 		
 		//get path related to mothur
-		string mothurPath = "";
 		for (int i = 0; i < dirs.size(); i++) {
 			//to lower so we can find it
 			string tempLower = "";
@@ -62,15 +54,53 @@ InteractEngine::InteractEngine(string path){
 			if (tempLower.find("mothur") != -1) {  mothurPath = dirs[i]; break;  }
 		}
 		
-		//add mothur so it looks like what argv would look like
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-			mothurPath += "/mothur";
-		#else
-			mothurPath += "\\mothur";
-		#endif
+		if (mothurPath != "") {
+			//add mothur so it looks like what argv would look like
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				mothurPath += "/mothur";
+			#else
+				mothurPath += "\\mothur";
+			#endif
+		}else {
+			//okay mothur is not in the path, so the folder mothur is in must be in the path
+			//lets find out which one
+			
+			//get path related to mothur
+			for (int i = 0; i < dirs.size(); i++) {
+								
+				//is this mothurs path?
+				ifstream in;
+				string tempIn = dirs[i];
+				#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+					tempIn += "/mothur";
+				#else
+					tempIn += "\\mothur";
+				#endif
+				mout->openInputFile(tempIn, in, "");
+				
+				//if this file exists
+				if (in) { in.close(); mothurPath = tempIn;  break;  }
+			}
+		}
+		
+		return mothurPath;
 		
-		path = mothurPath;
 	}
+	catch(exception& e) {
+		mout->errorOut(e, "Engine", "findMothursPath");
+		exit(1);
+	}
+}
+/***********************************************************************/
+
+InteractEngine::InteractEngine(string path){
+
+	globaldata = GlobalData::getInstance();
+	
+	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 = findMothursPath(); }
 	
 	globaldata->argv = path;
 }
@@ -152,6 +182,10 @@ bool InteractEngine::getInput(){
 					//executes valid command
 					Command* command = cFactory->getCommand(commandName, options);
 					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;
 										
@@ -181,7 +215,7 @@ string Engine::getCommand()  {
 				
 				if(nextCommand != NULL) {  add_history(nextCommand);  }	
 				else{ //^D causes null string and we want it to quit mothur
-					nextCommand = "quit"; 
+					strcpy(nextCommand, "quit"); 
 					mout->mothurOut(nextCommand);
 				}	
 				
@@ -218,48 +252,13 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 	try {
 		globaldata = GlobalData::getInstance();
 	
-		openedBatch = openInputFile(batchFileName, inputBatchFile);
+		openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
 		
-		string temppath = path.substr(0, (path.find_last_of('m')));
+		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 == "") { 
+		if (temppath == "") { path = findMothursPath(); }
 		
-			string envPath = getenv("PATH");
-			
-			//delimiting path char
-			char delim;
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-				delim = ':';
-			#else
-				delim = ';';
-			#endif
-			
-			//break apart path variable by ':'
-			vector<string> dirs;
-			splitAtChar(envPath, dirs, delim);
-			
-			//get path related to mothur
-			string mothurPath = "";
-			for (int i = 0; i < dirs.size(); i++) {
-				//to lower so we can find it
-				string tempLower = "";
-				for (int j = 0; j < dirs[i].length(); j++) {  tempLower += tolower(dirs[i][j]);  }
-				
-				//is this mothurs path?
-				if (tempLower.find("mothur") != -1) {  mothurPath = dirs[i]; break;  }
-			}
-			
-			//add mothur so it looks like what argv would look like
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-				mothurPath += "/mothur";
-			#else
-				mothurPath += "\\mothur";
-			#endif
-			
-			path = mothurPath;
-		}
-
 		globaldata->argv = path;
 				
 	}
@@ -291,7 +290,7 @@ bool BatchEngine::getInput(){
 		//CommandFactory cFactory;
 		int quitCommandCalled = 0;
 	    int count = 0;
-		while(quitCommandCalled == 0){
+		while(quitCommandCalled != 1){
 			
 			#ifdef USE_MPI
 				int pid, processors;
@@ -358,6 +357,10 @@ bool BatchEngine::getInput(){
 					//executes valid command
 					Command* command = cFactory->getCommand(commandName, options);
 					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;
 										
@@ -370,7 +373,7 @@ bool BatchEngine::getInput(){
 				}
 				
 			}
-			gobble(inputBatchFile);
+			mout->gobble(inputBatchFile);
 		}
 		
 		inputBatchFile.close();
@@ -388,7 +391,7 @@ string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 		string nextcommand = "";
 		
 		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
-		else { nextcommand = getline(inputBatchFile); }
+		else { nextcommand = mout->getline(inputBatchFile); }
 		
 		return nextcommand;
 	}
@@ -408,46 +411,11 @@ ScriptEngine::ScriptEngine(string path, string commandString){
 		//remove quotes
 		listOfCommands = commandString.substr(1, (commandString.length()-1));
 		
-		string temppath = path.substr(0, (path.find_last_of('m')));
-	
+		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 == "") { 
+		if (temppath == "") { path = findMothursPath(); }
 		
-			string envPath = getenv("PATH");
-			
-			//delimiting path char
-			char delim;
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-				delim = ':';
-			#else
-				delim = ';';
-			#endif
-			
-			//break apart path variable by ':'
-			vector<string> dirs;
-			splitAtChar(envPath, dirs, delim);
-			
-			//get path related to mothur
-			string mothurPath = "";
-			for (int i = 0; i < dirs.size(); i++) {
-				//to lower so we can find it
-				string tempLower = "";
-				for (int j = 0; j < dirs[i].length(); j++) {  tempLower += tolower(dirs[i][j]);  }
-				
-				//is this mothurs path?
-				if (tempLower.find("mothur") != -1) {  mothurPath = dirs[i]; break;  }
-			}
-			
-			//add mothur so it looks like what argv would look like
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-				mothurPath += "/mothur";
-			#else
-				mothurPath += "\\mothur";
-			#endif
-			
-			path = mothurPath;
-		}
-
 		globaldata->argv = path;
 				
 	}
@@ -474,7 +442,7 @@ bool ScriptEngine::getInput(){
 		//CommandFactory cFactory;
 		int quitCommandCalled = 0;
 	
-		while(quitCommandCalled == 0){
+		while(quitCommandCalled != 1){
 			
 			#ifdef USE_MPI
 				int pid, processors;
@@ -531,7 +499,6 @@ bool ScriptEngine::getInput(){
 					mout->executing = true;
 					#ifdef USE_MPI
 						int pid, numProcesses;
-						MPI_Status status; 
 						
 						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
 						MPI_Comm_size(MPI_COMM_WORLD, &numProcesses); 
@@ -543,6 +510,10 @@ bool ScriptEngine::getInput(){
 					//executes valid command
 					Command* command = cFactory->getCommand(commandName, options);
 					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;
 									
@@ -571,11 +542,16 @@ string ScriptEngine::getNextCommand(string& commandString) {
 		
 		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++;