added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / optionparser.h

diff --git a/optionparser.h b/optionparser.h
index b4d0dcb8691e103aa5c7259f3733d180e93cf29a..facd1f85182cc526a6db01d85968d9231afcfc88 100644 (file)
--- a/optionparser.h
+++ b/optionparser.h
@@ -13,16 +13,20 @@
 
 
 #include "mothur.h"
-
+#include "mothurout.h"
+#include "command.hpp"
 
 /***********************************************************************/
 
 class OptionParser {
-       public:
-               OptionParser() {}
-               ~OptionParser() {}
-               void parse(string, map<string, string>&);  //pass it an option string and a container
-                                                                                         //fills the container key=parameter name, value=parameter value
+public:
+       OptionParser(string);
+       ~OptionParser() {}
+       map<string, string> getParameters();
+       bool getNameFile(vector<string>);
+private:
+       map<string, string> parameters;
+       MothurOut* m;
 };
 
 /***********************************************************************/