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 "sequence.hpp"
  17 #include "dist.h"
  18
  19 struct Preference {
  20                 string name;
  21                 vector<string> leftParent; //keep the name of closest left associated with the two scores
  22                 vector<string> rightParent; //keep the name of closest right associated with the two scores
  23                 vector<float> score;  //so you can keep last score and calc this score and keep whichever is bigger.
  24                 vector<float> closestLeft;  //keep the closest left associated with the two scores
  25                 vector<float> closestRight; //keep the closest right associated with the two scores
  26                 int midpoint;
  27
  28 };
  29
  30
  31 /***********************************************************/
  32
  33 class Bellerophon : public Chimera {
  34
  35         public:
  36                 Bellerophon(string);
  37                 ~Bellerophon() {};
  38
  39                 void getChimeras();
  40                 void print(ostream&);
  41
  42                 void setCons(string){};
  43                 void setQuantiles(string) {};
  44
  45
  46         private:
  47                 Dist* distCalculator;
  48                 FilterSeqsCommand* filterSeqs;
  49                 vector<Sequence> seqs;
  50                 vector<Preference> pref;
  51                 string fastafile;
  52                 int iters;
  53
  54                 void readSeqs();
  55                 void generatePreferences(vector<SeqMap>, vector<SeqMap>, int);
  56                 int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
  57
  58
  59
  60
  61 };
  62
  63 /***********************************************************/
  64
  65 #endif
  66