5 * Created by Pat Schloss on 12/16/08.
6 * Copyright 2008 Patrick D. Schloss. All rights reserved.
8 * This is a basic alignment method that gets the blast program to do the heavy lifting. In the future, we should
9 * probably incorporate NCBI's library so that we don't have to call on a user-supplied executable. This is a child
10 * of the Alignment class, which requires a constructor and align method.
16 class BlastAlignment : public Alignment {
19 BlastAlignment(float, float, float, float);
21 void align(string, string);
24 string candidateFileName;
25 string templateFileName;
28 void setPairwiseSeqs();