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#ifndef NAST_HPP
#define NAST_HPP
/*
* nast.hpp
*
*
* Created by Pat Schloss on 12/17/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
* This is my implementation of the NAST (nearest alignment space termination) algorithm as described in:
*
* DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, & Anderson GL. 2006. NAST: a multiple
* sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research. 34:W394-9.
*
* To construct an object one needs to provide a method of getting a pairwise alignment (alignment) and the template
* and candidate sequence that are to be aligned to each other.
*
*/
#include "mothur.h"
#include "mothurout.h"
class Alignment;
class Sequence;
/**************************************************************************************************/
class Nast {
public:
Nast(Alignment*, Sequence*, Sequence*);
~Nast(){};
float getSimilarityScore();
int getMaxInsertLength();
private:
void pairwiseAlignSeqs();
void regapSequences();
void removeExtraGaps(string&, string, string);
Alignment* alignment;
Sequence* candidateSeq;
Sequence* templateSeq;
int maxInsertLength;
MothurOut* m;
};
/**************************************************************************************************/
#endif
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