working on chimeras

[mothur.git] / chimerarealigner.h

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
+