1 #ifndef HCLUSTERCOMMAND_H
2 #define HCLUSTERCOMMAND_H
8 * Created by westcott on 10/13/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "globaldata.hpp"
16 #include "rabundvector.hpp"
17 #include "sabundvector.hpp"
18 #include "listvector.hpp"
19 #include "readcluster.h"
21 /******************************************************************/
22 //This command is an implementation of the HCluster algorythmn described in
23 //ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences by
24 //Yijun Sun1,2,*, Yunpeng Cai2, Li Liu1, Fahong Yu1, Michael L. Farrell3, William McKendree3
25 //and William Farmerie1 1
27 //Interdisciplinary Center for Biotechnology Research, 2Department of Electrical and Computer Engineering,
28 //University of Florida, Gainesville, FL 32610-3622 and 3Materials Technology Directorate, Air Force Technical
29 //Applications Center, 1030 S. Highway A1A, Patrick AFB, FL 32925-3002, USA
30 //Received January 28, 2009; Revised April 14, 2009; Accepted April 15, 2009
31 /************************************************************/
32 class HClusterCommand : public Command {
35 HClusterCommand(string);
38 vector<string> getRequiredParameters();
39 vector<string> getValidParameters();
40 vector<string> getRequiredFiles();
41 map<string, vector<string> > getOutputFiles() { return outputTypes; }
46 GlobalData* globaldata;
50 RAbundVector oldRAbund;
54 bool abort, sorted, print_start, hard;
55 string method, fileroot, tag, distfile, format, phylipfile, columnfile, namefile, sort, showabund, timing, outputDir;
57 int precision, length;
58 ofstream sabundFile, rabundFile, listFile;
61 vector<string> outputNames;
62 map<string, vector<string> > outputTypes;
64 void printData(string label);
67 /************************************************************/