fixing minor bugs

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index e1bc23dfe4e800d74c9116b083b4eecf910e9e5b..df65678912b1f3bd112e630b13ef934eebc5e219 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -10,30 +10,17 @@
  *  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");
@@ -55,19 +42,19 @@ bool InteractEngine::getInput(){
        try {
                string input = "";
                string commandName = "";
+               string options = "";
                int quitCommandCalled = 0;
-               bool errorFree;
-               ErrorCheck* errorCheckor = new ErrorCheck();
+               //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;
@@ -76,18 +63,26 @@ bool InteractEngine::getInput(){
 
                        cout << endl << "mothur > ";
                        getline(cin, input);
-                       errorFree = errorCheckor->checkInput(input);
-                       if (errorFree == true) {
-                               CommandOptionParser parser(input);
-                               commandName = parser.getCommandString();
+                       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);
+                       commandName = parser.getCommandString();
+                       options = parser.getOptionString();
+                       
+                       if (commandName != "") {
                        
                                //executes valid command
                                CommandFactory cFactory;
-                               Command* command = cFactory.getCommand(commandName);
+                               Command* command = cFactory.getCommand(commandName, options);
                                quitCommandCalled = command->execute();
-               
+                               
                        }else {
-                                       cout << "Your input contains errors. Please try again." << endl;
+                               cout << "Your input contains errors. Please try again." << endl;
                        }
                }       
                return 1;
@@ -105,10 +100,11 @@ bool InteractEngine::getInput(){
 
 /***********************************************************************/
 //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");
        
@@ -138,37 +134,42 @@ BatchEngine::~BatchEngine(){
 //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;
-               ErrorCheck* errorCheckor = new ErrorCheck();
-
-               CommandFactory cFactory;
+               string options = "";
+               
+               //CommandFactory cFactory;
                int quitCommandCalled = 0;
        
                while(quitCommandCalled == 0){
                
-                       getline(inputBatchFile, input);
-                       cout << endl << "dotur > " << input << endl;
-                       errorFree = errorCheckor->checkInput(input);
-                       if (errorFree == true) {
+                       if (inputBatchFile.eof()) { input = "quit()"; }
+                       else { getline(inputBatchFile, input); }
+                       
+                       if (input[0] != '#') {
+                       
+                               cout << endl << "mothur > " << input << endl;
+                               
+                               //allow user to omit the () on the quit command
+                               if (input == "quit") { input = "quit()"; }
+
                                CommandOptionParser parser(input);
                                commandName = parser.getCommandString();
-                               ifstream filehandle;
-               
-                               if (openedBatch == 0) { //able to open batchfile
+                               options = parser.getOptionString();
+                                                                               
+                               if (commandName != "") {
+
                                        //executes valid command
                                        CommandFactory cFactory;
-                                       Command* command = cFactory.getCommand(commandName);
+                                       Command* command = cFactory.getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
-                               }
-                               else {
-                                       cout << "Invalid." << endl;
-                               }
-                       }
-                       else {
-                               cout << "Unable to open batchfile." << endl;
+                               }else {         cout << "Invalid." << endl;             }
+                               
                        }
+                       gobble(inputBatchFile);
                }
                return 1;
        }