broke up globaldata and moved error checking and help into commands

[mothur.git] / unifracunweightedcommand.h

diff --git a/unifracunweightedcommand.h b/unifracunweightedcommand.h
index 0a925385e3d6ef3f8621029038ebaafb1bfbec49..3c031c66c1da524e5b7f3177cfca7d0743573a7a 100644 (file)
--- a/unifracunweightedcommand.h
+++ b/unifracunweightedcommand.h
@@ -22,9 +22,10 @@ class GlobalData;
 class UnifracUnweightedCommand : public Command {
        
        public:
-               UnifracUnweightedCommand();     
+               UnifracUnweightedCommand(string);       
                ~UnifracUnweightedCommand() { delete unweighted; delete util; }
-               int execute();  
+               int execute();
+               void help();    
        
        private:
                GlobalData* globaldata;
@@ -46,6 +47,13 @@ class UnifracUnweightedCommand : 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;