X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=commandoptionparser.cpp;h=0038a714f4ae356e11d7dea57b4840a81eb946f4;hp=893d0d9cc0b043b5ccd6f37b45add01445e27152;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05

diff --git a/commandoptionparser.cpp b/commandoptionparser.cpp
index 893d0d9..0038a71 100644
--- a/commandoptionparser.cpp
+++ b/commandoptionparser.cpp
@@ -7,41 +7,36 @@
  *
  */
 
-#include <string>
 
-using namespace std;
-
-#include "globaldata.hpp"
 #include "commandoptionparser.hpp"
-#include <exception>
-#include <iostream>
+
 
 //**********************************************************************************************************************
 //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 ")".
+
+		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 ")".
 		}
-					
-		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) {
-		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);
 	}
-
 }
 
 //**********************************************************************************************************************
@@ -49,3 +44,7 @@ CommandOptionParser::CommandOptionParser(string input){
 string CommandOptionParser::getCommandString()	{	return commandString;	}
 
 //**********************************************************************************************************************
+
+string CommandOptionParser::getOptionString()	{	return optionString;	}
+
+//**********************************************************************************************************************