moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / nast.hpp

diff --git a/nast.hpp b/nast.hpp
deleted file mode 100644 (file)
index 9428aed..0000000
--- a/nast.hpp
+++ /dev/null
@@ -1,52 +0,0 @@
-#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