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[mothur.git] / clusterdoturcommand.h

diff --git a/clusterdoturcommand.h b/clusterdoturcommand.h
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+#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
+