fixes while testing 1.33.0

[mothur.git] / rarefactcommand.h

diff --git a/rarefactcommand.h b/rarefactcommand.h
index 7da0b2f9f5301d80302d97f7da23d1cd8fee12c1..02fe6e3aa4355a107e76f06d8f8f9a7f0df19118 100644 (file)
--- a/rarefactcommand.h
+++ b/rarefactcommand.h
@@ -14,48 +14,46 @@
 #include "inputdata.h"
 #include "rarefact.h"
 #include "display.h"
-#include "readotu.h"
 #include "validcalculator.h"
 
-
-class GlobalData;
-
 class RareFactCommand : public Command {
        
 public:
        RareFactCommand(string);
        RareFactCommand();      
-       ~RareFactCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();    
+       ~RareFactCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "rarefaction.single";          }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "Magurran AE (2004). Measuring biological diversity. Blackwell Pub.: Malden, Ma. \nhttp://www.mothur.org/wiki/Rarefaction.single"; }
+       string getDescription()         { return "generate intra-sample rarefaction curves using a re-sampling without replacement approach"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       GlobalData* globaldata;
+       
        vector<Display*> rDisplays;
-       ReadOTUFile* read;
        OrderVector* order;
        InputData* input;
-       ValidCalculators* validCalculator;
        Rarefact* rCurve;
        int nIters, abund, processors;
        float freq;
        
-       bool abort, allLines;
+       bool abort, allLines, groupMode;
        set<string> labels; //holds labels to be used
-       string label, calc;
+       string label, calc, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
        vector<string>  Estimators;
        vector<string> inputFileNames, outputNames;
        vector<string> groups;
-       map<string, vector<string> > outputTypes;
        string outputDir;
        
-       vector<string> parseSharedFile(string);
-
-
+       vector<string> parseSharedFile(string, map<string, set<int> >&);
+       vector<string> createGroupFile(vector<string>&, map<int, string>);
 };
 
 #endif