started shared utilities, updates to venn and heatmap added tree.groups command

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index e1bc23dfe4e800d74c9116b083b4eecf910e9e5b..68a75005f1521411227b20fe9ed253ec0b902e1c 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -12,20 +12,6 @@
  */
 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"
 
 /***********************************************************************/
@@ -59,15 +45,14 @@ bool InteractEngine::getInput(){
                bool errorFree;
                ErrorCheck* errorCheckor = new ErrorCheck();
                
-               cout << "MOTHUR v2.0 (Martha)" << endl;
-               cout << "Last updated: 1/07/2009" << endl << endl;
-               cout << "(Distance-based OTU and Richness)" << endl << endl;
+               cout << "mothur v1.0" << endl;
+               cout << "Last updated: 1/29/2009" << endl << endl;
                cout << "by" << endl;
                cout << "Patrick D. Schloss" << endl << endl;
                cout << "Department of Microbiology" << endl;
                cout << "The University of Massachusetts" << endl;
                cout << "pschloss@micro.umass.edu" << endl;
-               cout << "http://schloss.micro.umass.edu" << endl << endl << endl;
+               cout << "http://schloss.micro.umass.edu/mothur" << endl << endl << endl;
                cout << "Distributed under the GNU General Public License" << endl << endl;
                cout << "Type 'help()' for information on the commands that are available" << endl << endl;
                cout << "Type 'quit()' to exit program" << endl;
@@ -76,6 +61,8 @@ bool InteractEngine::getInput(){
 
                        cout << endl << "mothur > ";
                        getline(cin, input);
+                       if (cin.eof()) { input = "quit()"; }
+                       
                        errorFree = errorCheckor->checkInput(input);
                        if (errorFree == true) {
                                CommandOptionParser parser(input);
@@ -149,7 +136,9 @@ bool BatchEngine::getInput(){
                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);