X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=commandoptionparser.cpp;h=dfad533c8898ff3d79067d5f16c6869803e21e12;hp=f013a25361366bfecbecdccf0dd1d00c7805d16e;hb=615301e57c25e241356a9c2380648d117709458d;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2

diff --git a/commandoptionparser.cpp b/commandoptionparser.cpp
index f013a25..dfad533 100644
--- a/commandoptionparser.cpp
+++ b/commandoptionparser.cpp
@@ -8,7 +8,6 @@
  */
 
 
-#include "globaldata.hpp"
 #include "commandoptionparser.hpp"
 
 
@@ -16,23 +15,26 @@
 //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(')');
 		optionString = "";
 		commandString = "";
 
-		if(openParen != -1 && closeParen != -1){			
-			commandString = input.substr(0, openParen);   //commandString contains everything before "("
+		if(openParen != -1 && closeParen != -1){	
+            //gobble extra spaces
+            int spot = 0;
+            for (int i = 0; i < input.length(); i++) {  if (!(isspace(input[i]))) { spot = i; break; } }
+            if (spot > openParen) { spot = 0; }
+			commandString = input.substr(spot, openParen-spot);   //commandString contains everything before "("
 			optionString = input.substr((openParen+1), (closeParen-openParen-1)); //optionString contains everything between "(" and ")".
 		}
-		else if (openParen == -1) { mothurOut("You are missing ("); mothurOutEndLine(); }
-		else if (closeParen == -1) { mothurOut("You are missing )"); mothurOutEndLine(); }
-					
-		//GlobalData* globaldata = GlobalData::getInstance();
-		//globaldata->parseGlobalData(commandString, optionString);			//parser to separate and check options
-	}
+		else if (openParen == -1) { m->mothurOut("[ERROR]: You are missing ("); m->mothurOutEndLine(); }
+		else if (closeParen == -1) { m->mothurOut("[ERROR]:You are missing )"); m->mothurOutEndLine(); }
+    }
 	catch(exception& e) {
-		errorOut(e, "CommandOptionParser", "CommandOptionParser");
+		m->errorOut(e, "CommandOptionParser", "CommandOptionParser");
 		exit(1);
 	}
 }