fixed some bugs

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index 5e56479f2851f89e324f8c62dc54250324da7d66..d5192bf87b50a98a76e971305cd68a96e8750a0b 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -10,23 +10,17 @@
  *  Fix later, don't have time now.
  *
  */
-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");
@@ -52,8 +46,8 @@ bool InteractEngine::getInput(){
                bool errorFree;
                ErrorCheck* errorCheckor = new ErrorCheck();
                
-               cout << "mothur v1.0" << endl;
-               cout << "Last updated: 1/29/2009" << 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;
@@ -70,6 +64,9 @@ bool InteractEngine::getInput(){
                        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);
@@ -99,10 +96,11 @@ 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");
        
@@ -132,6 +130,9 @@ 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;
@@ -143,28 +144,34 @@ bool BatchEngine::getInput(){
                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;
+                               
+                               //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;
        }