broke up globaldata and moved error checking and help into commands

[mothur.git] / commandoptionparser.cpp

diff --git a/commandoptionparser.cpp b/commandoptionparser.cpp
index 6fc43ab9f44b980b677aa50bb8014a315fc34583..e4db11d1993f3ee257b36b010fb22944abc3b1cd 100644 (file)
--- a/commandoptionparser.cpp
+++ b/commandoptionparser.cpp
@@ -18,16 +18,18 @@ CommandOptionParser::CommandOptionParser(string input){
        try {
                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) { cout << "You are missing (" << endl; }
+               else if (closeParen == -1) { cout << "You are missing )" << endl; }
                                        
-               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";
@@ -45,3 +47,7 @@ CommandOptionParser::CommandOptionParser(string input){
 string CommandOptionParser::getCommandString() {       return commandString;   }
 
 //**********************************************************************************************************************
+
+string CommandOptionParser::getOptionString()  {       return optionString;    }
+
+//**********************************************************************************************************************