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

[mothur.git] / clusterdoturcommand.h

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
deleted file mode 100644 (file)
index 643551a..0000000
--- a/clusterdoturcommand.h
+++ /dev/null
@@ -1,54 +0,0 @@
-#ifndef CLUSTERDOTURCOMMAND_H
-#define CLUSTERDOTURCOMMAND_H
-
-/*
- *  clusterdoturcommand.h
- *  Mothur
- *
- *  Created by westcott on 10/27/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "nameassignment.hpp"
-#include "rabundvector.hpp"
-#include "sabundvector.hpp"
-#include "listvector.hpp"
-
-
-class ClusterDoturCommand : public Command {
-       
-public:
-       ClusterDoturCommand(string);
-       ClusterDoturCommand();
-       ~ClusterDoturCommand(){}
-       
-       vector<string> setParameters();
-       string getCommandName()                 { return "cluster.classic";             }
-       string getCommandCategory()             { return "Clustering";                  }
-       string getHelpString(); 
-       string getCitation() { return "Schloss PD, Handelsman J (2005). Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-6. \nhttp://www.mothur.org/wiki/Cluster.classic"; }
-       string getDescription()         { return "cluster your sequences into OTUs using DOTUR’s method"; }
-       
-       int execute(); 
-       void help() { m->mothurOut(getHelpString()); }  
-       
-private:
-       bool abort, hard, sim;
-       string method, fileroot, tag, outputDir, phylipfile, namefile;
-       double cutoff;
-       int precision, length;
-       ofstream sabundFile, rabundFile, listFile;
-       NameAssignment* nameMap;
-       ListVector* list;
-       RAbundVector* rabund;
-       RAbundVector oldRAbund;
-       ListVector oldList;
-       
-       void printData(string label);
-       vector<string> outputNames;
-};
-
-#endif
-