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

[mothur.git] / kmertree.h

diff --git a/kmertree.h b/kmertree.h
new file mode 100755 (executable)
index 0000000..f7c10ef
--- /dev/null
+++ b/kmertree.h
@@ -0,0 +1,37 @@
+//
+//  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