working on pam

[mothur.git] / commandoptionparser.cpp

diff --git a/commandoptionparser.cpp b/commandoptionparser.cpp
index e356afe5c74972e5298ddfa87a0672c97c4facfe..0038a714f4ae356e11d7dea57b4840a81eb946f4 100644 (file)
--- a/commandoptionparser.cpp
+++ b/commandoptionparser.cpp
@@ -22,16 +22,17 @@ CommandOptionParser::CommandOptionParser(string input){
                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) { m->mothurOut("[ERROR]: You are missing ("); m->mothurOutEndLine(); }
-               else if (closeParen == -1) { m->mothurOut("[ERROR]:You are missing )"); m->mothurOutEndLine(); }
-                                       
-               //GlobalData* globaldata = GlobalData::getInstance();
-               //globaldata->parseGlobalData(commandString, optionString);                     //parser to separate and check options
-       }
+               else if (closeParen == -1) { m->mothurOut("[ERROR]: You are missing )"); m->mothurOutEndLine(); }
+    }
        catch(exception& e) {
                m->errorOut(e, "CommandOptionParser", "CommandOptionParser");
                exit(1);