X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=kmertree.h;fp=kmertree.h;h=f7c10ef0797ad2ef376a98861b62004744cb3997;hb=e8e13c129ba8184ec5932a090773f353f3ae3406;hp=0000000000000000000000000000000000000000;hpb=035f86272c776e1cccaa47021e26782e49cd41e7;p=mothur.git

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+//
+//  kmerTree.h
+//  pdsBayesian
+//
+//  Created by Patrick Schloss on 4/3/12.
+//  Copyright (c) 2012 University of Michigan. All rights reserved.
+//
+
+#ifndef pdsBayesian_kmerTree_h
+#define pdsBayesian_kmerTree_h
+
+#include "classify.h"
+
+class KmerNode;
+
+class KmerTree : public Classify {
+	
+public:
+	KmerTree(string, string, int, int);
+	~KmerTree();
+	
+    string getTaxonomy(Sequence*);
+
+private:
+    int addTaxonomyToTree(string, string, vector<int>&);
+	vector<int> ripKmerProfile(string);
+	int getMinRiskIndexKmer(vector<int>&, vector<int>&, vector<double>&);
+	int aggregateThetas();
+	int sanityCheck(vector<vector<int> >&, vector<int>&);
+
+	int kmerSize;
+	int numPossibleKmers, confidenceThreshold;
+	vector<KmerNode*> tree;
+
+};
+
+#endif