Revert to previous commit

[mothur.git] / rarefactsharedcommand.h

diff --git a/rarefactsharedcommand.h b/rarefactsharedcommand.h
new file mode 100644 (file)
index 0000000..2112e8d
--- /dev/null
+++ b/rarefactsharedcommand.h
@@ -0,0 +1,53 @@
+#ifndef RAREFACTSHAREDCOMMAND_H
+#define RAREFACTSHAREDCOMMAND_H
+/*
+ *  rarefactsharedcommand.h
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 1/6/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "rarefact.h"
+#include "display.h"
+#include "validcalculator.h"
+
+class RareFactSharedCommand : public Command {
+       
+public:
+       RareFactSharedCommand(string);
+       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:
+       
+       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;
+
+};
+
+#endif