broke up globaldata and moved error checking and help into commands

[mothur.git] / venncommand.h

diff --git a/venncommand.h b/venncommand.h
index 663839c92ca560e8b5f657a775b634c83ef8af6d..3671350072afff05cf0816e66ce649182b00d258 100644 (file)
--- a/venncommand.h
+++ b/venncommand.h
@@ -23,9 +23,10 @@ class GlobalData;
 class VennCommand : public Command {
 
 public:
-       VennCommand();
+       VennCommand(string);
        ~VennCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -33,12 +34,21 @@ private:
        InputData* input;
        SharedListVector* SharedList;
        Venn* venn;
-       string format;
        vector<Calculator*> vennCalculators;    
        ValidCalculators* validCalculator;
        vector<SharedRAbundVector*> lookup;
        SAbundVector* sabund;
        int abund;
+       
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+       string format, groups, calc, line, label;
+       vector<string> Estimators, Groups;
+
 
 };