kmernode.h

   1 #ifndef KMERNODE
   2 #define KMERNODE
   3
   4 /*
   5  *  kmerNode.h
   6  *  bayesian
   7  *
   8  *  Created by Pat Schloss on 10/11/11.
   9  *  Copyright 2011 Patrick D. Schloss. All rights reserved.
  10  *
  11  */
  12
  13
  14 #include "taxonomynode.h"
  15
  16 /**********************************************************************************************************************/
  17
  18 class KmerNode : public TaxonomyNode {
  19
  20 public:
  21         KmerNode(string, int, int);
  22         void loadSequence(vector<int>&);
  23         void printTheta();
  24         double getPxGivenkj_D_j(vector<int>&);
  25         double getSimToConsensus(vector<int>&);
  26         void checkTheta(){};
  27         void setNumUniqueKmers(int num) {       numUniqueKmers = num;   }
  28         int getNumUniqueKmers();
  29         void addThetas(vector<int>, int);
  30         vector<int> getTheta()  {       return kmerVector;      }
  31
  32
  33 private:
  34         string getKmerBases(int);
  35         int kmerSize;                                                           //      value of k
  36         int numPossibleKmers;                                           //      4^kmerSize
  37         int numUniqueKmers;                                                     //      number of unique kmers seen in a group ~ O_kj
  38         int numKmers;                                                           //      number of kmers in a sequence
  39         vector<int> kmerVector;                                         //      counts of kmers across all sequences in a node
  40 };
  41
  42 /**********************************************************************************************************************/
  43
  44 #endif
  45