slayer.h

   1 #ifndef SLAYER_H
   2 #define SLAYER_H
   3 /*
   4  *  slayer.h
   5  *  Mothur
   6  *
   7  *  Created by westcott on 9/25/09.
   8  *  Copyright 2009 Schloss Lab. All rights reserved.
   9  *
  10  */
  11
  12
  13 #include "sequence.hpp"
  14 #include "chimera.h"
  15
  16 /***********************************************************************/
  17 //This class was modeled after the chimeraSlayer written by the Broad Institute
  18 /***********************************************************************/
  19 struct snps {
  20         char queryChar;
  21         char parentAChar;
  22         char parentBChar;
  23 };
  24
  25 /***********************************************************************/
  26
  27
  28 class Slayer {
  29
  30         public:
  31
  32                 Slayer(int, int, int, float, int, int, int);
  33                 ~Slayer() {};
  34
  35                 string getResults(Sequence, vector<Sequence>);
  36                 vector<data_struct> getOutput()  {      return outputResults;                   }
  37
  38
  39         private:
  40
  41                 int windowSize, windowStep, parentFragmentThreshold, iters, percentSNPSample, minBS;
  42                 float divRThreshold;
  43                 vector<data_struct>  outputResults;
  44                 vector< map<int, int> > baseSpots;
  45                 Sequence myQuery;
  46
  47                 map<int, int> verticalFilter(Sequence&, Sequence&, Sequence&);
  48                 float computePercentID(string, string, int, int);
  49
  50                 vector<data_struct> runBellerophon(Sequence, Sequence, Sequence, map<int, int>&);
  51                 vector<snps> getSNPS(string, string, string, int, int);
  52                 int bootstrapSNPS(vector<snps>, vector<snps>, float&, float&, int);
  53                 float snpQA(vector<snps>);
  54                 float snpQB(vector<snps>);
  55                 float snpAB(vector<snps>);
  56                 MothurOut* m;
  57
  58 };
  59
  60 /***********************************************************************/
  61
  62 #endif
  63
  64