broke up globaldata and moved error checking and help into commands

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index 603506f666e022a5b314aa73ca1e9817abfa85a4..bbcd6af5595d186610dae2818836d4d74b15f0f3 100644 (file)
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -22,9 +22,10 @@ class GlobalData;
 class ParsimonyCommand : public Command {
        
        public:
-               ParsimonyCommand();     
+               ParsimonyCommand(string);       
                ~ParsimonyCommand() { delete pars; delete util; delete output; }
                int execute();  
+               void help();
        
        private:
                GlobalData* globaldata;
@@ -55,6 +56,13 @@ class ParsimonyCommand : public Command {
                ofstream out, outSum;
                ifstream inFile;
                
+               OptionParser* parser;
+               map<string, string> parameters;
+               map<string, string>::iterator it4;
+               bool abort;
+               string groups, itersString;
+               vector<string> Groups; //holds groups to be used
+
                void printParsimonyFile();  
                void printUSummaryFile();
                void getUserInput();