added check to make sure shhh.flows child processes finish properly. added subsamplin...

[mothur.git] / rarefactsharedcommand.h

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index 7d4dc5edb76222095d0d650b93476e3218417044..1a2d944894feabe26b4103e5431c0da08c6574b4 100644 (file)
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -27,7 +27,8 @@ public:
        string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
        string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.shared"; }
-       
+       string getDescription()         { return "generate inter-sample rarefaction curves using a re-sampling without replacement approach"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
@@ -35,17 +36,16 @@ public:
 private:
        
        vector<SharedRAbundVector*> lookup;
-       InputData* input;
-       Rarefact* rCurve;
-       vector<Display*> rDisplays;
        int nIters;
        string format;
        float freq;
        
        bool abort, allLines, jumble;
        set<string> labels; //holds labels to be used
-       string label, calc, groups, outputDir, sharedfile;
-       vector<string>  Estimators, Groups, outputNames;
+       string label, calc, groups, outputDir, sharedfile, designfile;
+       vector<string>  Estimators, Groups, outputNames, Sets;
+    
+    int process(GroupMap&, string);
 
 };