X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mothur.cpp;h=0314331287f0de7c466dc5cb4aacedece62fd56a;hb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;hp=add60fa22f5c9a95137b651cf694dd6f27132ad7;hpb=36a8526766106bce1412e530e99f9c699dd59105;p=mothur.git

diff --git a/mothur.cpp b/mothur.cpp
index add60fa..0314331 100644
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -11,8 +11,6 @@
 #include "engine.hpp"
 #include "globaldata.hpp"
 
-using namespace std;
-
 /**************************************************************************************************/
 
 GlobalData* GlobalData::_uniqueInstance = 0;
@@ -24,9 +22,16 @@ int main(int argc, char *argv[]){
 
 		Engine* mothur;
 		bool bail = 0;
+		string input;
 
 		if(argc>1){
-			mothur = new BatchEngine(argv[0], argv[1]);
+			input = argv[1];
+
+			if (input[0] == '#') {
+				mothur = new ScriptEngine(argv[0], argv[1]);
+			}else{
+				mothur = new BatchEngine(argv[0], argv[1]);
+			}
 		}
 		else{
 			mothur = new InteractEngine(argv[0]);		
@@ -39,11 +44,7 @@ int main(int argc, char *argv[]){
 		return 0;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the dotur class Function main. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the dotur class function main. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "mothur", "main");
 		exit(1);
 	}
 }