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
  15 /***********************************************************************/
  16 //This class was modeled after the chimeraSlayer written by the Broad Institute
  17 /***********************************************************************/
  18 struct data_struct { //this is crazy big...but follow original.
  19         float divr_qla_qrb;
  20         float divr_qlb_qra;
  21         float qla_qrb;
  22         float qlb_qra;
  23         float qla;
  24         float qrb;
  25         float ab;
  26         float qa;
  27         float qb;
  28         float lab;
  29         float rab;
  30         float qra;
  31         float qlb;
  32         int winLStart;
  33         int winLEnd;
  34         int winRStart;
  35         int winREnd;
  36         Sequence querySeq;
  37         Sequence parentA;
  38         Sequence parentB;
  39         float bsa;
  40         float bsb;
  41         float bsMax;
  42         float chimeraMax;
  43
  44 };
  45 /***********************************************************************/
  46 //sorts lowest to highest first by bsMax, then if tie by chimeraMax
  47 inline bool compareDataStruct(data_struct left, data_struct right){
  48         if (left.bsMax < right.bsMax) { return true; }
  49         else if (left.bsMax == right.bsMax) {
  50                 return (left.chimeraMax < right.chimeraMax);
  51         }else { return false;   }
  52 }
  53 /***********************************************************************/
  54 struct snps {
  55         char queryChar;
  56         char parentAChar;
  57         char parentBChar;
  58 };
  59
  60 /***********************************************************************/
  61
  62
  63 class Slayer {
  64
  65         public:
  66
  67                 Slayer(int, int, int, float, int, int);
  68                 ~Slayer() {};
  69
  70                 string getResults(Sequence*, vector<Sequence*>);
  71                 vector<data_struct> getOutput()  {      return outputResults;                   }
  72
  73
  74         private:
  75
  76                 int windowSize, windowStep, parentFragmentThreshold, iters, percentSNPSample;
  77                 float divRThreshold;
  78                 vector<data_struct>  outputResults;
  79                 vector< map<int, int> > baseSpots;
  80
  81                 map<int, int> verticalFilter(vector<Sequence*>);
  82                 float computePercentID(string, string, int, int);
  83
  84                 vector<data_struct> runBellerophon(Sequence*, Sequence*, Sequence*, map<int, int>&);
  85                 vector<snps> getSNPS(string, string, string, int, int);
  86                 int bootstrapSNPS(vector<snps>, vector<snps>, float&, float&);
  87                 float snpQA(vector<snps>);
  88                 float snpQB(vector<snps>);
  89                 float snpAB(vector<snps>);
  90                 MothurOut* m;
  91
  92 };
  93
  94 /***********************************************************************/
  95
  96 #endif
  97
  98