X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandoptionparser.cpp;h=df216da738e7ba6dd92ec0817c6353b0b1723870;hb=9bc68cbe7fd7c5cf00b66d73d60624de80fb7933;hp=a46c0a6ccfc47859d06ae6cae21e87a441be460c;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d;p=mothur.git

diff --git a/commandoptionparser.cpp b/commandoptionparser.cpp
index a46c0a6..df216da 100644
--- a/commandoptionparser.cpp
+++ b/commandoptionparser.cpp
@@ -8,9 +8,6 @@
  */
 
 
-using namespace std;
-
-
 #include "globaldata.hpp"
 #include "commandoptionparser.hpp"
 
@@ -19,28 +16,27 @@ using namespace std;
 //This Function parses through the command line and pulls out the command then sends the options to  the parseGlobalData
 CommandOptionParser::CommandOptionParser(string input){
 	try {
+		m = MothurOut::getInstance();
+		
 		int openParen = input.find_first_of('(');
 		int closeParen = input.find_last_of(')');
-		string optionString = "";
+		optionString = "";
 		commandString = "";
-	
+
 		if(openParen != -1 && closeParen != -1){			
 			commandString = input.substr(0, openParen);   //commandString contains everything before "("
-			optionString = input.substr(openParen+1, closeParen-openParen-1); //optionString contains everything between "(" and ")".
+			optionString = input.substr((openParen+1), (closeParen-openParen-1)); //optionString contains everything between "(" and ")".
 		}
+		else if (openParen == -1) { m->mothurOut("You are missing ("); m->mothurOutEndLine(); }
+		else if (closeParen == -1) { m->mothurOut("You are missing )"); m->mothurOutEndLine(); }
 					
-		GlobalData* globaldata = GlobalData::getInstance();
-		globaldata->parseGlobalData(commandString, optionString);			//parser to separate and check options
+		//GlobalData* globaldata = GlobalData::getInstance();
+		//globaldata->parseGlobalData(commandString, optionString);			//parser to separate and check options
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the CommandOptionParser class Function CommandOptionParser. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the CommandOptionParser class function CommandOptionParser. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "CommandOptionParser", "CommandOptionParser");
 		exit(1);
 	}
-
 }
 
 //**********************************************************************************************************************
@@ -48,3 +44,7 @@ CommandOptionParser::CommandOptionParser(string input){
 string CommandOptionParser::getCommandString()	{	return commandString;	}
 
 //**********************************************************************************************************************
+
+string CommandOptionParser::getOptionString()	{	return optionString;	}
+
+//**********************************************************************************************************************