bellerophon.h

   1 #ifndef BELLEROPHON_H
   2 #define BELLEROPHON_H
   3
   4 /*
   5  *  bellerophon.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 7/9/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "chimera.h"
  15 #include "filterseqscommand.h"
  16 #include "sparsematrix.hpp"
  17 #include "sequence.hpp"
  18 #include "dist.h"
  19
  20 typedef list<PCell>::iterator MatData;
  21 typedef map<int, float> SeqMap;  //maps sequence to all distance for that seqeunce
  22
  23 /***********************************************************/
  24
  25 class Bellerophon : public Chimera {
  26
  27         public:
  28                 Bellerophon(string, string);
  29                 ~Bellerophon() {};
  30
  31                 int getChimeras();
  32                 void print(ostream&);
  33
  34                 void setCons(string){};
  35                 void setQuantiles(string) {};
  36
  37
  38         private:
  39                 Dist* distCalculator;
  40                 FilterSeqsCommand* filterSeqs;
  41                 vector<Sequence*> seqs;
  42                 vector<Preference> pref;
  43                 string fastafile;
  44                 int iters;
  45
  46                 void generatePreferences(vector<SeqMap>, vector<SeqMap>, int);
  47                 int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
  48 };
  49
  50 /***********************************************************/
  51
  52 #endif
  53