broke up globaldata and moved error checking and help into commands

[mothur.git] / unifracweightedcommand.h

diff --git a/unifracweightedcommand.h b/unifracweightedcommand.h
index 491d3846f65ae135d458c947b3f4a7539a5acde8..2d78d57fe827a0678421f39a44c0d2e6fe4cedf0 100644 (file)
--- a/unifracweightedcommand.h
+++ b/unifracweightedcommand.h
@@ -23,9 +23,10 @@ class GlobalData;
 class UnifracWeightedCommand : public Command {
        
        public:
-               UnifracWeightedCommand();       
+               UnifracWeightedCommand(string); 
                ~UnifracWeightedCommand() { delete weighted; delete util; }
                int execute();  
+               void help();
        
        private:
                GlobalData* globaldata;
@@ -50,6 +51,14 @@ class UnifracWeightedCommand : public Command {
                map<float, float>::iterator it2;
                map<float, float>::iterator it;
                
+               OptionParser* parser;
+               map<string, string> parameters;
+               map<string, string>::iterator it4;
+               bool abort;
+               string groups, itersString;
+               vector<string> Groups; //holds groups to be used
+
+               
                ofstream outSum, out;
                ifstream inFile;