added alignment code

[mothur.git] / nast.hpp

diff --git a/nast.hpp b/nast.hpp
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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"
+
+class Alignment;
+class Sequence;
+
+/**************************************************************************************************/
+
+class Nast {
+       
+public:
+       Nast(Alignment*, Sequence*, Sequence*);
+       float getSimilarityScore();
+       int getMaxInsertLength();
+       
+private:
+       void pairwiseAlignSeqs();
+       void regapSequences();
+       void removeExtraGaps(string&, string, string);
+       
+       Alignment* alignment;
+       Sequence* candidateSeq;
+       Sequence* templateSeq;
+       
+       int maxInsertLength;
+};
+
+/**************************************************************************************************/
+
+#endif