X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerarealigner.h;fp=chimerarealigner.h;h=2b53841e241806c435a0a8f30b7c444b6050739f;hb=5a1e62397b91f57d0d3aff635891df04b8999a88;hp=0000000000000000000000000000000000000000;hpb=df92022fc75c08b91cefa2c6ca4fd7b23eb480b0;p=mothur.git

diff --git a/chimerarealigner.h b/chimerarealigner.h
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+#ifndef CHIMERAREALIGNER_H
+#define CHIMERAREALIGNER_H
+
+/*
+ *  chimerarealigner.h
+ *  Mothur
+ *
+ *  Created by westcott on 2/12/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "chimera.h"
+#include "alignment.hpp"
+
+/***********************************************************/
+
+class ChimeraReAligner  {
+	
+	public:
+		ChimeraReAligner(vector<Sequence*>, int, int);	 
+		~ChimeraReAligner();
+		
+		void reAlign(Sequence*, vector<results>);
+				
+	private:
+		Sequence* querySeq;
+		Alignment* alignment;
+		vector<Sequence*> templateSeqs;
+		int match, misMatch;
+		
+		Sequence* getSequence(string);  //find sequence from name
+};
+/***********************************************************/
+
+#endif
+