X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=blastalign.hpp;fp=blastalign.hpp;h=0f755d852cb0fdb793c40e88613dd8b19076c991;hb=526a868606faa50caf86e7399f7554c0335b39e5;hp=0000000000000000000000000000000000000000;hpb=c35f02a218ce8f430a75850b4d9fabb96b3a022b;p=mothur.git

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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;
+};
+