moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / rarefactcommand.h

diff --git a/rarefactcommand.h b/rarefactcommand.h
deleted file mode 100644 (file)
index 6aaa3de..0000000
--- a/rarefactcommand.h
+++ /dev/null
@@ -1,57 +0,0 @@
-#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