alignedsimilarity.h

   1 #ifndef ALIGNSIM_H
   2 #define ALIGNSIM_H
   3
   4 /*
   5  *  alignedsimilarity.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 8/18/09.
   9  *  Copyright 2009 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "chimera.h"
  15 #include "dist.h"
  16
  17 //This class was created using the algorythms described in the
  18 //"Evaluation of Nearest Neighbor Methods for Detection of Chimeric Small-Subunit rRna Sequences" paper
  19 //by J.F. Robison-Cox 1, M.M. Bateson 2 and D.M. Ward 2
  20
  21
  22 /***********************************************************/
  23
  24 class AlignSim : public Chimera {
  25
  26         public:
  27                 AlignSim(string, string);
  28                 ~AlignSim();
  29
  30                 void getChimeras();
  31                 void print(ostream&);
  32
  33                 void setCons(string){};
  34                 void setQuantiles(string q) { quanfile = q; };
  35
  36
  37         private:
  38
  39                 Dist* distCalc;
  40                 vector<linePair*> lines;
  41                 vector<linePair*> templateLines;
  42
  43                 vector<Sequence*> querySeqs;
  44                 vector<Sequence*> templateSeqs;
  45
  46                 vector< vector<sim> > IS;  //IS[0] is the vector os sim values for each window for querySeqs[0]
  47                 vector< vector<sim> > templateIS;  //templateIS[0] is the vector os sim values for each window for templateSeqs[0]
  48                 vector<int> windowBreak;
  49
  50                 string fastafile, templateFile;
  51                 int iters;
  52
  53                 vector< vector<sim> > findIS(int, int, vector<Sequence*>);
  54                 vector<Sequence*> findClosestSides(Sequence*, int, vector<int>&, int);
  55                 int findNumMatchedBases(Sequence, Sequence);
  56                 vector<int> findWindows();
  57
  58                 vector< vector<float> > quantile;
  59
  60                 vector< vector<sim> > createProcessesIS(vector<Sequence*>, vector<linePair*>);
  61
  62 };
  63
  64 /***********************************************************/
  65
  66 #endif
  67