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/*  (c) Centro de Regulacio Genomica                                                        */
/*  and                                                                                     */
/*  Cedric Notredame                                                                        */
/*  12 Aug 2014 - 22:07.                                                                    */
/*All rights reserved.                                                                      */
/*This file is part of T-COFFEE.                                                            */
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/*  If you need some more information                                                       */
/*  cedric.notredame@europe.com                                                             */
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typedef struct
{
	///field saving the positions [x1,y1,l1,x2,y2,l2,...]
	int *segments;
	/// points to the current used segment
 	int *current_pos;
	/// saves the previous diagonal position.
	int prev_position;
	/// diagonal number
// 	int diagonal_num;
}
Segment;


Segment* extend_diagonals(Diagonal *diagonals, int *num_diagonals, int l1, int l2);
int seq_pair2blast_diagonal2(char *seq_file_name1, char *seq_file_name2, Diagonal **diagonals, int *dig_length, int l1, int l2, int is_dna);

int ** segments2int(Segment *diagonals, int num_diagonals, char *seq1, char *seq2, Fastal_profile *profile1, Fastal_profile *profile2, int *num_points, Fastal_param *param_set);