X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerarealigner.h;fp=chimerarealigner.h;h=5809f42997381ab53ba5aaeb43a6c0d0b5cb6619;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;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"
+
+/***********************************************************/
+
+struct AlignCell {
+	int score;
+	char direction;
+	AlignCell() : score(0), direction('x') {};
+};
+
+/***********************************************************/
+
+struct  bases {
+	int A, T, G, C, Gap, Chars;
+	bases() : A(0), T(0), G(0), C(0), Gap(0), Chars(0){};
+};
+
+/***********************************************************/
+
+
+class ChimeraReAligner  {
+	
+public:
+	ChimeraReAligner();	 
+	~ChimeraReAligner();
+	
+	void reAlign(Sequence*, vector<string>);
+				
+private:
+	void buildTemplateProfile(vector<string>);
+	void createAlignMatrix(int, int);
+	void fillAlignMatrix(string);
+	int calcMatchScore(bases, char);
+	string getNewAlignment(string);
+
+	int alignmentLength;
+	vector<bases> profile;
+	vector<vector<AlignCell> > alignMatrix;
+
+	MothurOut* m;
+};
+
+/***********************************************************/
+
+#endif
+