* 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");
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 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;
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()"; }
+
+ //allow user to omit the () on the quit command
+ if (input == "quit") { 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");
//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;
while(quitCommandCalled == 0){
getline(inputBatchFile, input);
- cout << endl << "dotur > " << input << endl;
- errorFree = errorCheckor->checkInput(input);
- if (errorFree == true) {
- CommandOptionParser parser(input);
- commandName = parser.getCommandString();
- ifstream filehandle;
+ if (input[0] != '#') {
+ if (inputBatchFile.eof()) { input = "quit()"; }
+
+ 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;
}