ccode.h

   1 #ifndef CCODE_H
   2 #define CCODE_H
   3
   4 /*
   5  *  ccode.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 8/24/09.
   9  *  Copyright 2009 Schloss LAB. All rights reserved.
  10  *
  11  */
  12
  13 #include "chimera.h"
  14 #include "dist.h"
  15 #include "decalc.h"
  16
  17 //This class was created using the algorythms described in the
  18 // "Evaluating putative chimeric sequences from PCR-amplified products" paper
  19 //by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.
  20
  21 /***********************************************************/
  22
  23 class Ccode : public Chimera {
  24
  25         public:
  26                 Ccode(string, string);
  27                 ~Ccode();
  28
  29                 void getChimeras();
  30                 void print(ostream&);
  31
  32                 void setCons(string c)          {}
  33                 void setQuantiles(string q) {}
  34
  35
  36         private:
  37
  38                 Dist* distCalc;
  39                 DeCalculator* decalc;
  40                 int iters;
  41                 string fastafile, templateFile;
  42
  43
  44                 vector<linePair*> lines;
  45                 vector<linePair*> templateLines;
  46                 vector<Sequence*> querySeqs;
  47                 vector<Sequence*> templateSeqs;
  48
  49                 vector<int> windows;
  50                 vector< vector<Sequence*> > closest;  //closest[0] is a vector of sequence at are closest to queryseqs[0]...
  51                 vector< vector<float> > averageRef;  //averageRef[0] is the average distance at each window for the references for querySeqs[0]
  52                 vector< vector<float> > averageQuery;  //averageQuery[0] is the average distance at each winow for the query for querySeqs[0]
  53
  54                 vector< vector<Sequence*> > findClosest(int, int, int);
  55                 void removeBadReferenceSeqs(vector<Sequence*>&, int);  //removes sequences from closest that are to different of too similar to eachother.
  56                 void trimSequences();
  57                 vector<int> findWindows();
  58                 vector<float> getAverageRef(vector<Sequence*>);
  59                 vector<float> getAverageQuery (vector<Sequence*>, int);
  60
  61
  62                 int getDiff(string, string);  //return number of mismatched bases, a gap to base is not counted as a mismatch
  63
  64                 void createProcessesClosest();
  65
  66 };
  67
  68 /***********************************************************/
  69
  70 #endif
  71
  72