X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=a90bb7e0588baee4f8d922687f99063c8d961387;hb=e99751591aa21705e58edda87383457b9738dd9e;hp=7bacec5c0e757c7b77d3c8801970c17bd3cc5a4a;hpb=9013e13ecfb2fda3c2664a76f76cc99b8c7fa74c;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index 7bacec5..a90bb7e 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -31,8 +31,48 @@ Engine::Engine(){
 InteractEngine::InteractEngine(string path){
 
 	globaldata = GlobalData::getInstance();
-	globaldata->argv = path;
 	
+	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 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;
+		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 = "";
+			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;
 }
 
 /***********************************************************************/
@@ -178,7 +218,48 @@ 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')));
+	
+		//this will happen if you set the path variable to contain mothur's exe location
+		if (temppath == "") { 
+		
+			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;
+			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 = "";
+				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;
 				
 	}
@@ -289,7 +370,7 @@ bool BatchEngine::getInput(){
 				}
 				
 			}
-			gobble(inputBatchFile);
+			mout->gobble(inputBatchFile);
 		}
 		
 		inputBatchFile.close();
@@ -307,7 +388,7 @@ string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 		string nextcommand = "";
 		
 		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
-		else { nextcommand = getline(inputBatchFile); }
+		else { nextcommand = mout->getline(inputBatchFile); }
 		
 		return nextcommand;
 	}
@@ -326,6 +407,46 @@ 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')));
+	
+		//this will happen if you set the path variable to contain mothur's exe location
+		if (temppath == "") { 
+		
+			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;
+			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 = "";
+				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;
 				
@@ -450,11 +571,16 @@ 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++;