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