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.
15 #include "globaldata.hpp"
17 class BlastAlignment : public Alignment {
20 BlastAlignment(float, float, float, float);
22 void align(string, string);
25 string candidateFileName;
26 string templateFileName;
30 void setPairwiseSeqs();
35 GlobalData* globaldata;