X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=df65678912b1f3bd112e630b13ef934eebc5e219;hb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;hp=e251f0031d5ffa2bc9685702ef76ae0489af8449;hpb=16bea3130e36addc54e2116dfbcd02d706ebee45;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index e251f00..df65678 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -10,30 +10,17 @@
  *  Fix later, don't have time now.
  *
  */
-using namespace std;
-
-#include <string>
-#include <iostream>
-#include <iomanip>
-#include <fstream>
-#include <vector>
-#include <set>
-#include <exception>
-
-#include "utilities.hpp"
-#include "globaldata.hpp"
-#include "commandoptionparser.hpp"
-#include "command.hpp"
-#include "commandfactory.hpp"
-#include "errorchecking.h"
+
+
 #include "engine.hpp"
 
 /***********************************************************************/
 
-InteractEngine::InteractEngine(){
+InteractEngine::InteractEngine(string path){
 
 	globaldata = GlobalData::getInstance();
-
+	globaldata->argv = path;
+	
 	system("clear");
 //	char buffer = ' ';
 //	ifstream header("introtext.txt");
@@ -55,12 +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 v1.0" << endl;
-		cout << "Last updated: 1/29/2009" << 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;
@@ -77,18 +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;
@@ -106,10 +100,11 @@ 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");
 	
@@ -139,39 +134,42 @@ 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;
-		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] != '#') {
 			
-			cout << endl << "mothur > " << input << endl;
-			errorFree = errorCheckor->checkInput(input);
-			if (errorFree == true) {
+				cout << endl << "mothur > " << input << endl;
+				
+				//allow user to omit the () on the quit command
+				if (input == "quit") { input = "quit()"; }
+
 				CommandOptionParser parser(input);
 				commandName = parser.getCommandString();
-				ifstream filehandle;
-		
-				if (openedBatch == 0) { //able to open batchfile
+				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 << "Invalid." << endl;
-				}
-			}
-			else {
-				cout << "Unable to open batchfile." << endl;
+				}else {		cout << "Invalid." << endl;		}
+				
 			}
+			gobble(inputBatchFile);
 		}
 		return 1;
 	}