X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=593c2c3128d08cfe8abddfa81a1e384a1d17aa62;hb=c82900be3ceed3d9bc491bdc98b1819ef85c1af7;hp=55617bc3f80a97e1832ff61c3e09678de8eca1ca;hpb=29c0d3ec01be5372807eb86261100d77de253787;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index 55617bc..593c2c3 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -14,20 +14,28 @@
 
 #include "engine.hpp"
 
+/***********************************************************************/
+Engine::Engine(){
+	try {
+		cFactory = CommandFactory::getInstance();
+	}
+	catch(exception& e) {
+		errorOut(e, "Engine", "Engine");
+		exit(1);
+	}
+}
+
 /***********************************************************************/
 
 InteractEngine::InteractEngine(string path){
 
 	globaldata = GlobalData::getInstance();
 	globaldata->argv = path;
-	
-	system("clear");
 }
 
 /***********************************************************************/
 
-InteractEngine::~InteractEngine(){
-	}
+InteractEngine::~InteractEngine(){}
 
 /***********************************************************************/
 //This function allows the user to input commands one line at a time until they quit.
@@ -39,29 +47,24 @@ bool InteractEngine::getInput(){
 		string options = "";
 		int quitCommandCalled = 0;
 		
-				
 		while(quitCommandCalled != 1){
-			
+
 			mothurOutEndLine();
-			mothurOut("mothur > ");
-			getline(cin, input);
-			if (cin.eof()) { input = "quit()"; }
 			
-			mothurOutJustToLog(input);
-			mothurOutEndLine();
+			input = getCommand();			
 			
 			//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 != "") {
 			
 				//executes valid command
-				CommandFactory cFactory;
-				Command* command = cFactory.getCommand(commandName, options);
+				Command* command = cFactory->getCommand(commandName, options);
 				quitCommandCalled = command->execute();
 				
 			}else {
@@ -76,7 +79,37 @@ bool InteractEngine::getInput(){
 		exit(1);
 	}
 }
-
+/***********************************************************************/
+string Engine::getCommand()  {
+	try {
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#ifdef USE_READLINE
+				char* nextCommand = NULL;
+				nextCommand = readline("mothur > ");
+				if(nextCommand != NULL) {  add_history(nextCommand);  }		
+				mothurOutJustToLog("mothur > " + toString(nextCommand));
+				return nextCommand;
+			#else
+				string nextCommand = "";
+				mothurOut("mothur > ");
+				getline(cin, nextCommand);
+				return nextCommand;
+			#endif
+		#else
+			string nextCommand = "";
+			mothurOut("mothur > ");
+			getline(cin, nextCommand);
+			return nextCommand;
+		#endif
+		
+		mothurOutEndLine();
+						
+	}
+	catch(exception& e) {
+		errorOut(e, "Engine", "getCommand");
+		exit(1);
+	}
+}
 /***********************************************************************/
 //This function opens the batchfile to be used by BatchEngine::getInput.
 BatchEngine::BatchEngine(string path, string batchFileName){
@@ -86,14 +119,6 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 		openedBatch = openInputFile(batchFileName, inputBatchFile);
 		globaldata->argv = path;
 				
-		system("clear");
-	
-	//	char buffer = ' ';
-	//	ifstream header("introtext.txt");
-	//	while(!header.eof()){
-	//		cout << buffer;
-	//		buffer = header.get();
-	//	}
 	}
 	catch(exception& e) {
 		errorOut(e, "BatchEngine", "BatchEngine");
@@ -103,8 +128,7 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 
 /***********************************************************************/
 
-BatchEngine::~BatchEngine(){
-	}
+BatchEngine::~BatchEngine(){	}
 
 /***********************************************************************/
 //This Function allows the user to run a batchfile containing several commands on Dotur
@@ -127,9 +151,7 @@ bool BatchEngine::getInput(){
 		while(quitCommandCalled == 0){
 	
 			if (inputBatchFile.eof()) { input = "quit()"; }
-			else { getline(inputBatchFile, input); }
-			
-			
+			else { input = getline(inputBatchFile); }
 			
 			if (input[0] != '#') {
 				
@@ -148,8 +170,7 @@ bool BatchEngine::getInput(){
 				if (commandName != "") {
 
 					//executes valid command
-					CommandFactory cFactory;
-					Command* command = cFactory.getCommand(commandName, options);
+					Command* command = cFactory->getCommand(commandName, options);
 					quitCommandCalled = command->execute();
 				}else {		
 					mothurOut("Invalid."); 
@@ -182,8 +203,6 @@ ScriptEngine::ScriptEngine(string path, string commandString){
 
 		globaldata->argv = path;
 		
-		system("clear");
-	
 	}
 	catch(exception& e) {
 		errorOut(e, "ScriptEngine", "ScriptEngine");
@@ -193,8 +212,7 @@ ScriptEngine::ScriptEngine(string path, string commandString){
 
 /***********************************************************************/
 
-ScriptEngine::~ScriptEngine(){
-	}
+ScriptEngine::~ScriptEngine(){ 	}
 
 /***********************************************************************/
 //This Function allows the user to run a batchfile containing several commands on mothur
@@ -231,8 +249,7 @@ bool ScriptEngine::getInput(){
 			if (commandName != "") {
 
 				//executes valid command
-				CommandFactory cFactory;
-				Command* command = cFactory.getCommand(commandName, options);
+				Command* command = cFactory->getCommand(commandName, options);
 				quitCommandCalled = command->execute();
 			}else {		
 				mothurOut("Invalid."); 
@@ -252,13 +269,21 @@ bool ScriptEngine::getInput(){
 string ScriptEngine::getNextCommand(string& commandString) {
 	try {
 		string nextcommand = "";
+		int count = 0;
 		
-		nextcommand = commandString.substr(0,commandString.find_first_of(';'));
-
+		//go through string until you reach ; or end
+		while (count < commandString.length()) { 
+			
+			if (commandString[count] == ';') {  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) {