X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerarealigner.h;fp=chimerarealigner.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=5809f42997381ab53ba5aaeb43a6c0d0b5cb6619;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/chimerarealigner.h b/chimerarealigner.h
deleted file mode 100644
index 5809f42..0000000
--- a/chimerarealigner.h
+++ /dev/null
@@ -1,59 +0,0 @@
-#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
-