broke up globaldata and moved error checking and help into commands

[mothur.git] / libshuffcommand.h

diff --git a/libshuffcommand.h b/libshuffcommand.h
index 07c1ba5ceb732c52ce825419c8173f1746e10435..150bdb4aecdfeeae4b91b6e0152eb812dca846ea 100644 (file)
--- a/libshuffcommand.h
+++ b/libshuffcommand.h
@@ -20,9 +20,10 @@ class GlobalData;
 class LibShuffCommand : public Command {
        
        public:
-               LibShuffCommand();      
+               LibShuffCommand(string);        
                ~LibShuffCommand(){};
-               int execute();  
+               int execute();
+               void help();    
        
        private:
                vector<string> groupNames;
@@ -40,6 +41,12 @@ class LibShuffCommand : public Command {
                vector<vector<int> > pValueCounts;
                vector<vector<double> > savedDXYValues;
                vector<vector<vector<double> > > savedMinValues;
+               OptionParser* parser;
+               map<string, string> parameters;
+               map<string, string>::iterator it;
+               bool abort;
+               string outputFile, groups, userform, savegroups;
+               vector<string> Groups; //holds groups to be used
 };
 
 #endif