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//
// 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*, string&, bool&);
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
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