added alignment code

[mothur.git] / blastalign.hpp

diff --git a/blastalign.hpp b/blastalign.hpp
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+/*
+ *  blastalign.hpp
+ *  
+ *
+ *  Created by Pat Schloss on 12/16/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ *     This is a basic alignment method that gets the blast program to do the heavy lifting.  In the future, we should
+ *     probably incorporate NCBI's library so that we don't have to call on a user-supplied executable.  This is a child
+ *     of the Alignment class, which requires a constructor and align method.
+ *
+ */
+ 
+#include "mothur.h"
+
+class BlastAlignment : public Alignment {
+
+public:
+       BlastAlignment(float, float, float, float);
+       ~BlastAlignment();
+       void align(string, string);
+private:
+
+       string candidateFileName;
+       string templateFileName;
+       string blastFileName;
+
+       void setPairwiseSeqs();
+       float match;
+       float mismatch;
+       float gapOpen;
+       float gapExtend;
+};
+