*/
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");
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 v1.2.0" << endl;
+ cout << "Last updated: 4/14/2009" << 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;
cout << endl << "mothur > ";
getline(cin, input);
+ if (cin.eof()) { input = "quit()"; }
+
errorFree = errorCheckor->checkInput(input);
if (errorFree == true) {
CommandOptionParser parser(input);
/***********************************************************************/
//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");
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);