*/
using namespace std;
-#include <string>
-#include <iostream>
-#include <iomanip>
-#include <fstream>
-#include <vector>
-#include <set>
-#include <exception>
#include "utilities.hpp"
#include "globaldata.hpp"
cout << endl << "mothur > ";
getline(cin, input);
+ if (cin.eof()) { input = "quit()"; }
+
errorFree = errorCheckor->checkInput(input);
if (errorFree == true) {
CommandOptionParser parser(input);
while(quitCommandCalled == 0){
getline(inputBatchFile, input);
- cout << endl << "dotur > " << input << endl;
+ if (inputBatchFile.eof()) { input = "quit()"; }
+
+ cout << endl << "mothur > " << input << endl;
errorFree = errorCheckor->checkInput(input);
if (errorFree == true) {
CommandOptionParser parser(input);