added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / rarefactsharedcommand.h

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
index da26d174ca3c3cc9da41027f5252aa8f58288f20..2112e8d78565712a490de69bedd2ffb44844a768 100644 (file)
--- a/rarefactsharedcommand.h
+++ b/rarefactsharedcommand.h
@@ -13,36 +13,41 @@
 #include "inputdata.h"
 #include "rarefact.h"
 #include "display.h"
-#include "readotu.h"
 #include "validcalculator.h"
 
-class GlobalData;
-
 class RareFactSharedCommand : public Command {
        
 public:
        RareFactSharedCommand(string);
-       ~RareFactSharedCommand();
-       int execute();  
-       void help();
+       RareFactSharedCommand();
+       ~RareFactSharedCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "rarefaction.shared";          }
+       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()); }  
+       
        
 private:
-       GlobalData* globaldata;
-       ReadOTUFile* read;
+       
        vector<SharedRAbundVector*> lookup;
        InputData* input;
-       ValidCalculators* validCalculator;
        Rarefact* rCurve;
        vector<Display*> rDisplays;
-       int freq, nIters;
+       int nIters;
        string format;
-
+       float freq;
+       
        bool abort, allLines, jumble;
        set<string> labels; //holds labels to be used
-       string label, calc, groups, outputDir;
+       string label, calc, groups, outputDir, sharedfile;
        vector<string>  Estimators, Groups, outputNames;
 
-
 };
 
 #endif