mallard.h

   1 #ifndef MALLARD_H
   2 #define MALLARD_H
   3
   4 /*
   5  *  mallard.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 8/11/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "chimera.h"
  15 #include "decalc.h"
  16
  17 //This class was created using the algorythms described in the
  18 // "New Screening Software Shows that Most Recent Large 16SrRNA Gene Clone Libraries Contain Chimeras" paper
  19 //by Kevin E. Ashelford 1, Nadia A. Chuzhanova 2, John C. Fry 1, Antonia J. Jones 3 and Andrew J. Weightman 1.
  20
  21 /***********************************************************/
  22
  23 class Mallard : public Chimera {
  24
  25         public:
  26                 Mallard(string);
  27                 ~Mallard();
  28
  29                 void getChimeras();
  30                 void print(ostream&);
  31
  32                 void setCons(string c)  {};
  33                 void setQuantiles(string q) {};
  34
  35         private:
  36
  37                 struct linePair {
  38                         int start;
  39                         int end;
  40                         linePair(int i, int j) : start(i), end(j) {}
  41                         linePair(){}
  42                 };
  43
  44                 DeCalculator* decalc;
  45                 int iters;
  46                 string fastafile;
  47
  48                 vector<linePair*> lines;
  49                 vector<Sequence*> querySeqs;
  50                 vector<int> windowSizes;                        //windowSizes[0] = window size of querySeqs[0]
  51                 vector<int> marked;
  52                 vector<float> highestDE;
  53
  54                 vector<float> probabilityProfile;
  55                 vector< vector<quanMember> > quantilesMembers;  //quantiles[0] is the vector of deviations with ceiling score of 1, quantiles[1] is the vector of deviations with ceiling score of 2...
  56
  57                 void createProcessesQuan();
  58
  59 };
  60
  61 /***********************************************************/
  62
  63 #endif
  64