]> git.donarmstrong.com Git - mothur.git/blobdiff - rarefactsharedcommand.h
removed read.dist, read.otu, read.tree and globaldata. added current to defaults...
[mothur.git] / rarefactsharedcommand.h
index ee16221903ce2ee738cd7b941ca90c5b57e05c04..8219e613b3c71d657deb31deb8a948f501dc6e52 100644 (file)
 #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();
-       ~RareFactSharedCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help();
+       ~RareFactSharedCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "rarefaction.shared";          }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       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 nIters;
@@ -45,10 +43,8 @@ private:
        
        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;
-       map<string, vector<string> > outputTypes;
-
 
 };