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 "globaldata.hpp"
18 #include "cluster.hpp"
21 /**********************************************************************/
23 class MGClusterCommand : public Command {
26 MGClusterCommand(string);
32 GlobalData* globaldata;
34 NameAssignment* nameMap;
39 vector<seqDist> overlapMatrix;
41 string blastfile, method, namefile, overlapFile, distFile, outputDir;
42 ofstream sabundFile, rabundFile, listFile;
43 float cutoff, penalty;
44 int precision, length, precisionLength;
45 bool abort, minWanted, hclusterWanted, merge;
47 void printData(ListVector*);
48 ListVector* mergeOPFs(map<string, int>, float);
49 void sortHclusterFiles(string, string);
50 vector<seqDist> getSeqs(ifstream&);
54 /**********************************************************************/