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

[mothur.git] / hclustercommand.h

diff --git a/hclustercommand.h b/hclustercommand.h
deleted file mode 100644 (file)
index aeeb3bc..0000000
--- a/hclustercommand.h
+++ /dev/null
@@ -1,71 +0,0 @@
-#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