broke up globaldata and moved error checking and help into commands

[mothur.git] / rarefactcommand.h

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 5ac970ee8542b7d0793734d56d813afe506e1e09..ea867f091415354864af382505df75e97d67294a 100644 (file)
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -37,9 +37,10 @@ class GlobalData;
 class RareFactCommand : public Command {
        
 public:
-       RareFactCommand();      
+       RareFactCommand(string);        
        ~RareFactCommand();
-       int execute();  
+       int execute();
+       void help();    
        
 private:
        GlobalData* globaldata;
@@ -50,6 +51,15 @@ private:
        ValidCalculators* validCalculator;
        Rarefact* rCurve;
        int freq, nIters, 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 line, label, calc;
+       vector<string>  Estimators;
+
 };
 
 #endif