X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=d5192bf87b50a98a76e971305cd68a96e8750a0b;hb=df82ee669d7eb9ae9a1a334339dfab7961cb16c6;hp=b9360a4468a9aedd553675d9d3a2110afa6feab7;hpb=e2373397d9316500ee0d196e60dcab75d208511a;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index b9360a4..d5192bf 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -10,16 +10,17 @@
  *  Fix later, don't have time now.
  *
  */
-using namespace std;
+
 
 #include "engine.hpp"
 
 /***********************************************************************/
 
-InteractEngine::InteractEngine(){
+InteractEngine::InteractEngine(string path){
 
 	globaldata = GlobalData::getInstance();
-
+	globaldata->argv = path;
+	
 	system("clear");
 //	char buffer = ' ';
 //	ifstream header("introtext.txt");
@@ -45,8 +46,8 @@ bool InteractEngine::getInput(){
 		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;
@@ -63,6 +64,9 @@ bool InteractEngine::getInput(){
 			getline(cin, input);
 			if (cin.eof()) { input = "quit()"; }
 			
+			//allow user to omit the () on the quit command
+			if (input == "quit") { input = "quit()"; }
+			
 			errorFree = errorCheckor->checkInput(input);
 			if (errorFree == true) {
 				CommandOptionParser parser(input);
@@ -92,10 +96,11 @@ bool InteractEngine::getInput(){
 
 /***********************************************************************/
 //This function opens the batchfile to be used by BatchEngine::getInput.
-BatchEngine::BatchEngine(string batchFileName){
+BatchEngine::BatchEngine(string path, string batchFileName){
 	try {
 		globaldata = GlobalData::getInstance();
 		openedBatch = openInputFile(batchFileName, inputBatchFile);
+		globaldata->argv = path;
 
 		system("clear");
 	
@@ -125,6 +130,9 @@ BatchEngine::~BatchEngine(){
 //This Function allows the user to run a batchfile containing several commands on Dotur
 bool BatchEngine::getInput(){
 	try {
+		//check if this is a valid batchfile
+		if (openedBatch == 1) {  cout << "unable to open batchfile" << endl;  return 1; }
+	
 		string input = "";
 		string commandName = "";
 		bool errorFree;
@@ -136,28 +144,34 @@ bool BatchEngine::getInput(){
 		while(quitCommandCalled == 0){
 		
 			getline(inputBatchFile, input);
-			if (inputBatchFile.eof()) { input = "quit()"; }
+			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;
+				cout << endl << "mothur > " << input << endl;
+				
+				//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();
+					ifstream filehandle;
 		
-				if (openedBatch == 0) { //able to open batchfile
-					//executes valid command
-					CommandFactory cFactory;
-					Command* command = cFactory.getCommand(commandName);
-					quitCommandCalled = command->execute();
+					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 << "Invalid." << endl;
+					cout << "Unable to open batchfile." << endl;
 				}
-			}
-			else {
-				cout << "Unable to open batchfile." << endl;
-			}
+			}else { if (inputBatchFile.eof()) { input = "quit()"; } }
 		}
 		return 1;
 	}