1 #ifndef GETOTUREPCOMMAND_H
2 #define GETOTUREPCOMMAND_H
7 * Created by Sarah Westcott on 4/6/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 #include "command.hpp"
13 #include "globaldata.hpp"
14 #include "sparsematrix.hpp"
15 #include "listvector.hpp"
16 #include "inputdata.h"
17 #include "readmatrix.hpp"
23 typedef list<PCell>::iterator MatData;
25 class GetOTURepCommand : public Command {
33 GlobalData* globaldata;
36 ListVector* listOfNames;
40 string filename, fastafile, namesfile;
45 map<string, int> nameToIndex; //maps sequence name to index in sparsematrix
46 map<int, string>::iterator it;
47 map<int, string>::iterator it2;
48 map<string, int>::iterator it3;
51 string FindRep(int); // returns name of "representative" sequence of given bin.