8 * Created by Sarah Westcott on 7/9/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
15 #include "filterseqscommand.h"
16 #include "sparsematrix.hpp"
17 #include "sequence.hpp"
20 typedef list<PCell>::iterator MatData;
21 typedef map<int, float> SeqMap; //maps sequence to all distance for that seqeunce
23 /***********************************************************/
25 class Bellerophon : public Chimera {
28 Bellerophon(string, string);
32 int print(ostream&, ostream&);
36 FilterSeqsCommand* filterSeqs;
37 vector<Sequence*> seqs;
38 vector<Preference> pref;
42 int generatePreferences(vector<SeqMap>, vector<SeqMap>, int);
43 int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
46 /***********************************************************/