broke up globaldata and moved error checking and help into commands

[mothur.git] / optionparser.cpp

diff --git a/optionparser.cpp b/optionparser.cpp
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+++ b/optionparser.cpp
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+/*
+ *  optionparser.cpp
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 6/8/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "optionparser.h"
+
+/***********************************************************************/
+void OptionParser::parse(string option, map<string, string>& container) {
+       try {
+               
+               if (option != "") {
+               
+                       string key, value;              
+                       //reads in parameters and values
+                       while((option.find_first_of(',') != -1)) {  //while there are parameters
+                                       splitAtComma(value, option);
+                                       splitAtEquals(key, value);
+                                       container[key] = value;
+                       }
+               
+                       //in case there is no comma and to get last parameter after comma
+                       splitAtEquals(key, option);
+                       container[key] = option;
+               }
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the OptionParser class Function parse. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the OptionParser class function parse. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+/***********************************************************************/
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