X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=kmernode.h;fp=kmernode.h;h=e15fb1d29ec136c1edc1914629a53389aab568fb;hb=e8e13c129ba8184ec5932a090773f353f3ae3406;hp=0000000000000000000000000000000000000000;hpb=035f86272c776e1cccaa47021e26782e49cd41e7;p=mothur.git diff --git a/kmernode.h b/kmernode.h new file mode 100755 index 0000000..e15fb1d --- /dev/null +++ b/kmernode.h @@ -0,0 +1,45 @@ +#ifndef KMERNODE +#define KMERNODE + +/* + * kmerNode.h + * bayesian + * + * Created by Pat Schloss on 10/11/11. + * Copyright 2011 Patrick D. Schloss. All rights reserved. + * + */ + + +#include "taxonomynode.h" + +/**********************************************************************************************************************/ + +class KmerNode : public TaxonomyNode { + +public: + KmerNode(string, int, int); + void loadSequence(vector&); + void printTheta(); + double getPxGivenkj_D_j(vector&); + double getSimToConsensus(vector&); + void checkTheta(){}; + void setNumUniqueKmers(int num) { numUniqueKmers = num; } + int getNumUniqueKmers(); + void addThetas(vector, int); + vector getTheta() { return kmerVector; } + + +private: + string getKmerBases(int); + int kmerSize; // value of k + int numPossibleKmers; // 4^kmerSize + int numUniqueKmers; // number of unique kmers seen in a group ~ O_kj + int numKmers; // number of kmers in a sequence + vector kmerVector; // counts of kmers across all sequences in a node +}; + +/**********************************************************************************************************************/ + +#endif +