added zap method to classify.seqs and changed bayesian method name to wang.

[mothur.git] / kmernode.h

diff --git a/kmernode.h b/kmernode.h
new file mode 100755 (executable)
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<int>&);
+       void printTheta();
+       double getPxGivenkj_D_j(vector<int>&);
+       double getSimToConsensus(vector<int>&);
+       void checkTheta(){};
+       void setNumUniqueKmers(int num) {       numUniqueKmers = num;   }
+       int getNumUniqueKmers();
+       void addThetas(vector<int>, int);
+       vector<int> 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<int> kmerVector;                                         //      counts of kmers across all sequences in a node
+};
+
+/**********************************************************************************************************************/
+
+#endif
+