1 #ifndef BlastAlignment_H
2 #define BlastAlignment_H
3 
4 
5 /*
6  *  blastalign.hpp
7  *
8  *
9  *  Created by Pat Schloss on 12/16/08.
10  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
11  *
12  *	This is a basic alignment method that gets the blast program to do the heavy lifting.  In the future, we should
13  *	probably incorporate NCBI's library so that we don't have to call on a user-supplied executable.  This is a child
14  *	of the Alignment class, which requires a constructor and align method.
15  *
16  */
17 
18 #include "mothur.h"
19 
20 
21 class BlastAlignment : public Alignment {
22 
23 public:
24 	BlastAlignment(float, float, float, float);
25 	~BlastAlignment();
26 	void align(string, string, bool createBaseMap=false);
setMatrix(int)27 	void setMatrix(int){};
28 
29 private:
30 
31 	string candidateFileName;
32 	string templateFileName;
33 	string blastFileName;
34 	string path;
35 
36 	void setPairwiseSeqs();
37 	float match;
38 	float mismatch;
39 	float gapOpen;
40 	float gapExtend;
41 };
42 
43 #endif
44 
45 
46 
47