X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=df65678912b1f3bd112e630b13ef934eebc5e219;hb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;hp=11d738dd0f2384b42a26f21349eeaa7bbca80a2a;hpb=825512fb96e5bb00e08665396d9fa6a8c4da5a68;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index 11d738d..df65678 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -10,7 +10,7 @@
  *  Fix later, don't have time now.
  *
  */
-using namespace std;
+
 
 #include "engine.hpp"
 
@@ -42,12 +42,13 @@ bool InteractEngine::getInput(){
 	try {
 		string input = "";
 		string commandName = "";
+		string options = "";
 		int quitCommandCalled = 0;
-		bool errorFree;
-		ErrorCheck* errorCheckor = new ErrorCheck();
+		//bool errorFree;
+		//ErrorCheck* errorCheckor = new ErrorCheck();
 		
-		cout << "mothur v1.2.0" << endl;
-		cout << "Last updated: 4/14/2009" << endl << endl;
+		cout << "mothur v.1.3.0" << endl;
+		cout << "Last updated: 5/29/2009" << endl << endl;
 		cout << "by" << endl;
 		cout << "Patrick D. Schloss" << endl << endl;
 		cout << "Department of Microbiology" << endl;
@@ -64,18 +65,24 @@ bool InteractEngine::getInput(){
 			getline(cin, input);
 			if (cin.eof()) { input = "quit()"; }
 			
-			errorFree = errorCheckor->checkInput(input);
-			if (errorFree == true) {
-				CommandOptionParser parser(input);
-				commandName = parser.getCommandString();
+			//allow user to omit the () on the quit command
+			if (input == "quit") { input = "quit()"; }
+			
+			//errorFree = errorCheckor->checkInput(input);
+			//if (errorFree == true) {
+			CommandOptionParser parser(input);
+			commandName = parser.getCommandString();
+			options = parser.getOptionString();
+			
+			if (commandName != "") {
 			
 				//executes valid command
 				CommandFactory cFactory;
-				Command* command = cFactory.getCommand(commandName);
+				Command* command = cFactory.getCommand(commandName, options);
 				quitCommandCalled = command->execute();
-		
+				
 			}else {
-					cout << "Your input contains errors. Please try again." << endl;
+				cout << "Your input contains errors. Please try again." << endl;
 			}
 		}	
 		return 1;
@@ -132,39 +139,37 @@ bool BatchEngine::getInput(){
 	
 		string input = "";
 		string commandName = "";
-		bool errorFree;
-		ErrorCheck* errorCheckor = new ErrorCheck();
-
-		CommandFactory cFactory;
+		string options = "";
+		
+		//CommandFactory cFactory;
 		int quitCommandCalled = 0;
 	
 		while(quitCommandCalled == 0){
 		
-			getline(inputBatchFile, input);
+			if (inputBatchFile.eof()) { input = "quit()"; }
+			else { getline(inputBatchFile, input); }
+			
 			if (input[0] != '#') {
-				if (inputBatchFile.eof()) { input = "quit()"; }
 			
 				cout << endl << "mothur > " << input << endl;
-				errorFree = errorCheckor->checkInput(input);
-				if (errorFree == true) {
-					CommandOptionParser parser(input);
-					commandName = parser.getCommandString();
-					ifstream filehandle;
-		
-					if (openedBatch == 0) { //able to open batchfile
-						//executes valid command
-						CommandFactory cFactory;
-						Command* command = cFactory.getCommand(commandName);
-						quitCommandCalled = command->execute();
-					}
-					else {
-						cout << "Invalid." << endl;
-					}
-				}
-				else {
-					cout << "Unable to open batchfile." << endl;
-				}
-			}else { if (inputBatchFile.eof()) { 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 != "") {
+
+					//executes valid command
+					CommandFactory cFactory;
+					Command* command = cFactory.getCommand(commandName, options);
+					quitCommandCalled = command->execute();
+				}else {		cout << "Invalid." << endl;		}
+				
+			}
+			gobble(inputBatchFile);
 		}
 		return 1;
 	}