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[mothur.git] / hclustercommand.h

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+#ifndef HCLUSTERCOMMAND_H
+#define HCLUSTERCOMMAND_H
+
+/*
+ *  hclustercommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 10/13/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+#include "hcluster.h"
+#include "rabundvector.hpp"
+#include "sabundvector.hpp"
+#include "listvector.hpp"
+#include "readcluster.h"
+
+/******************************************************************/
+//This command is an implementation of the HCluster algorythmn described in 
+//ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences by
+//Yijun Sun1,2,*, Yunpeng Cai2, Li Liu1, Fahong Yu1, Michael L. Farrell3, William McKendree3 
+//and William Farmerie1 1 
+
+//Interdisciplinary Center for Biotechnology Research, 2Department of Electrical and Computer Engineering, 
+//University of Florida, Gainesville, FL 32610-3622 and 3Materials Technology Directorate, Air Force Technical 
+//Applications Center, 1030 S. Highway A1A, Patrick AFB, FL 32925-3002, USA 
+//Received January 28, 2009; Revised April 14, 2009; Accepted April 15, 2009 
+/************************************************************/
+class HClusterCommand : public Command {
+       
+public:
+       HClusterCommand(string);
+       HClusterCommand();      
+       ~HClusterCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "hcluster";    }
+       string getCommandCategory()             { return "Clustering";  }
+       string getHelpString(); 
+       string getCitation() { return "Sun Y, Cai Y, Liu L, Yu F, Farrell ML, Mckendree W, Farmerie W (2009). ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res 37: e76. \nhttp://www.mothur.org/wiki/Hcluster"; }
+       string getDescription()         { return "cluster your sequences into OTUs using a distance matrix"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
+private:
+       HCluster* cluster;
+       ListVector* list;
+       RAbundVector* rabund;
+       RAbundVector oldRAbund;
+       ListVector oldList;
+       ReadCluster* read;
+       
+       bool abort, sorted, print_start, hard;
+       string method, fileroot, tag, distfile, format, phylipfile, columnfile, namefile, sort, showabund, timing, outputDir;
+       double cutoff;
+       int precision, length;
+       ofstream sabundFile, rabundFile, listFile;
+       time_t start;
+       unsigned long loops;
+       vector<string> outputNames;
+       
+       void printData(string label);
+};
+
+/************************************************************/
+
+#endif