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

[mothur.git] / aligntree.h

diff --git a/aligntree.h b/aligntree.h
new file mode 100755 (executable)
index 0000000..51008ff
--- /dev/null
+++ b/aligntree.h
@@ -0,0 +1,34 @@
+//
+//  alignTree.h
+//  pdsBayesian
+//
+//  Created by Patrick Schloss on 4/3/12.
+//  Copyright (c) 2012 University of Michigan. All rights reserved.
+//
+
+#ifndef pdsBayesian_alignTree_h
+#define pdsBayesian_alignTree_h
+
+#include "classify.h"
+
+class AlignNode;
+
+class AlignTree : public Classify {
+
+public:
+       AlignTree(string, string, int);
+       ~AlignTree();
+       string getTaxonomy(Sequence*);
+       
+private:
+    int addTaxonomyToTree(string, string&, string&);
+       double getOutlierLogProbability(string&);
+       int getMinRiskIndexAlign(string&, vector<int>&, vector<double>&);
+       int aggregateThetas();
+       int sanityCheck(vector<vector<int> >&, vector<int>&);
+
+       int numSeqs, confidenceThreshold, length;
+       vector<AlignNode*> tree;
+};
+
+#endif