*/
using namespace std;
-
-#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 v1.0" << endl;
- cout << "Last updated: 1/29/2009" << 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;
/***********************************************************************/
//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);
- if (inputBatchFile.eof()) { input = "quit()"; }
+ if (input[0] != '#') {
+ if (inputBatchFile.eof()) { input = "quit()"; }
- cout << endl << "mothur > " << input << endl;
- errorFree = errorCheckor->checkInput(input);
- if (errorFree == true) {
- CommandOptionParser parser(input);
- commandName = parser.getCommandString();
- ifstream filehandle;
+ cout << endl << "mothur > " << input << endl;
+ 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;
}