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 { //not right needs work...
  19         int regionStart;
  20         int regionEnd;
  21         string parent;
  22         float queryToParent;
  23         float queryToParentLocal;
  24         float divR;
  25 };
  26 /***********************************************************************/
  27
  28
  29 class Slayer {
  30
  31         public:
  32
  33                 Slayer(int, int, int, float);
  34                 ~Slayer() {};
  35
  36                 void getResults(Sequence*, vector<Sequence*>);
  37                 //float getPercentID() {        return percentIdenticalQueryChimera;    }
  38                 //vector<results> getOutput()  {        return outputResults;                   }
  39
  40
  41         private:
  42
  43                 int windowSize, windowStep, parentFragmentThreshold;
  44                 float divRThreshold;
  45
  46                 void verticalFilter(vector<Sequence*>);
  47                 float computePercentID(string, string, int, int);
  48
  49                 vector<data_struct> runBellerophon(Sequence*, Sequence*, Sequence*);
  50
  51
  52 };
  53
  54 /***********************************************************************/
  55
  56 #endif
  57
  58