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[mothur.git] / rarefactcommand.h

diff --git a/rarefactcommand.h b/rarefactcommand.h
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+#ifndef RAREFACTCOMMAND_H
+#define RAREFACTCOMMAND_H
+/*
+ *  rarefactcommand.h
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/2/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "ordervector.hpp"
+#include "inputdata.h"
+#include "rarefact.h"
+#include "display.h"
+#include "validcalculator.h"
+
+class RareFactCommand : public Command {
+       
+public:
+       RareFactCommand(string);
+       RareFactCommand();      
+       ~RareFactCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "rarefaction.single";          }
+       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.single"; }
+       string getDescription()         { return "generate intra-sample rarefaction curves using a re-sampling without replacement approach"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       
+       vector<Display*> rDisplays;
+       OrderVector* order;
+       InputData* input;
+       Rarefact* rCurve;
+       int nIters, abund, processors;
+       float freq;
+       
+       bool abort, allLines, groupMode;
+       set<string> labels; //holds labels to be used
+       string label, calc, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
+       vector<string>  Estimators;
+       vector<string> inputFileNames, outputNames;
+       vector<string> groups;
+       string outputDir;
+       
+       vector<string> parseSharedFile(string);
+       vector<string> createGroupFile(vector<string>&, map<int, string>);
+};
+
+#endif