changes to dist.seqs and pairwise.seqs and cluster.classic no longer resizes

[mothur.git] / optionparser.cpp

diff --git a/optionparser.cpp b/optionparser.cpp
index 2de1621bcb9a73ac9c17b02384ee6d9b0f3f5d49..08032b32b83556f7ace0b83e235e51121e80f399 100644 (file)
--- a/optionparser.cpp
+++ b/optionparser.cpp
@@ -13,28 +13,24 @@
 
 OptionParser::OptionParser(string option) {
        try {
-               
+               m = MothurOut::getInstance();
                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);
+                               m->splitAtComma(value, option);
+                               m->splitAtEquals(key, value);
                                parameters[key] = value;
                        }
                        
                        //in case there is no comma and to get last parameter after comma
-                       splitAtEquals(key, option);
+                       m->splitAtEquals(key, option);
                        parameters[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";
+               m->errorOut(e, "OptionParser", "parse");
                exit(1);
        }
 }