added trim.seqs command

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index ac49206040520592a212b68594305cf464494155..d5192bf87b50a98a76e971305cd68a96e8750a0b 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -10,7 +10,7 @@
  *  Fix later, don't have time now.
  *
  */
-using namespace std;
+
 
 #include "engine.hpp"
 
@@ -46,8 +46,8 @@ bool InteractEngine::getInput(){
                bool errorFree;
                ErrorCheck* errorCheckor = new ErrorCheck();
                
-               cout << "mothur v1.2.0" << endl;
-               cout << "Last updated: 4/14/2009" << 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;
@@ -64,6 +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);
@@ -127,6 +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;
@@ -142,6 +148,10 @@ bool BatchEngine::getInput(){
                                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);