8 * Created by Pat Schloss on 12/17/08.
9 * Copyright 2008 Patrick D. Schloss. All rights reserved.
11 * This is my implementation of the NAST (nearest alignment space termination) algorithm as described in:
13 * DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, & Anderson GL. 2006. NAST: a multiple
14 * sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research. 34:W394-9.
16 * To construct an object one needs to provide a method of getting a pairwise alignment (alignment) and the template
17 * and candidate sequence that are to be aligned to each other.
26 /**************************************************************************************************/
31 Nast(Alignment*, Sequence*, Sequence*);
33 float getSimilarityScore();
34 int getMaxInsertLength();
37 void pairwiseAlignSeqs();
38 void regapSequences();
39 void removeExtraGaps(string&, string, string);
42 Sequence* candidateSeq;
43 Sequence* templateSeq;
48 /**************************************************************************************************/