1 #ifndef CHIMERAREALIGNER_H
2 #define CHIMERAREALIGNER_H
8 * Created by westcott on 2/12/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "alignment.hpp"
16 /***********************************************************/
21 AlignCell() : score(0), direction('x') {};
24 /***********************************************************/
27 int A, T, G, C, Gap, Chars;
28 bases() : A(0), T(0), G(0), C(0), Gap(0), Chars(0){};
31 /***********************************************************/
34 class ChimeraReAligner {
40 void reAlign(Sequence*, vector<string>);
43 void buildTemplateProfile(vector<string>);
44 void createAlignMatrix(int, int);
45 void fillAlignMatrix(string);
46 int calcMatchScore(bases, char);
47 string getNewAlignment(string);
50 vector<bases> profile;
51 vector<vector<AlignCell> > alignMatrix;
56 /***********************************************************/