1 #ifndef MGCLUSTERCOMMAND_H
2 #define MGCLUSTERCOMMAND_H
8 * Created by westcott on 12/11/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "readblast.h"
15 #include "sparsematrix.hpp"
16 #include "nameassignment.hpp"
17 #include "cluster.hpp"
19 #include "rabundvector.hpp"
20 #include "sabundvector.hpp"
22 /**********************************************************************/
24 class MGClusterCommand : public Command {
27 MGClusterCommand(string);
31 vector<string> setParameters();
32 string getCommandName() { return "mgcluster"; }
33 string getCommandCategory() { return "Clustering"; }
34 string getHelpString();
35 string getCitation() { return "Schloss PD, Handelsman J (2008). A statistical toolbox for metagenomics. BMC Bioinformatics 9: 34. \nhttp://www.mothur.org/wiki/Mgcluster"; }
38 void help() { m->mothurOut(getHelpString()); }
43 NameAssignment* nameMap;
48 vector<seqDist> overlapMatrix;
49 vector<string> outputNames;
51 string blastfile, method, namefile, overlapFile, distFile, outputDir;
52 ofstream sabundFile, rabundFile, listFile;
55 int precision, length, precisionLength;
56 bool abort, minWanted, hclusterWanted, merge, hard;
58 void printData(ListVector*);
59 ListVector* mergeOPFs(map<string, int>, float);
60 void sortHclusterFiles(string, string);
61 vector<seqDist> getSeqs(ifstream&);
65 /**********************************************************************/