/******************************COPYRIGHT NOTICE*******************************/
/*  (c) Centro de Regulacio Genomica                                                        */
/*  and                                                                                     */
/*  Cedric Notredame                                                                        */
/*  30 Nov 2019 - 10:22.                                                                    */
/*All rights reserved.                                                                      */
/*This file is part of T-COFFEE.                                                            */
/*                                                                                          */
/*    T-COFFEE is free software; you can redistribute it and/or modify                      */
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/*    (at your option) any later version.                                                   */
/*                                                                                          */
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/*    GNU General Public License for more details.                                          */
/*                                                                                          */
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/*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
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/*  If you need some more information                                                       */
/*  cedric.notredame@gmail.com                                                             */
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void seq2profile2(char *seq, Fastal_profile *prf, int *char2pos);
void split_set(FILE *aln_file_name, Fastal_profile *gap_prf, Fastal_profile *no_gap_prf, char *seq, int index, int *char2pos, char* split_file_name);
void iterate(Fastal_param *param, void *method_arguments_p, char *aln_file_name, char *out_file_name, int iteration_number);

void edit2seq_pattern(FILE *edit_file, char *seq1, char *seq2);
int *del_gap_from_profile(Fastal_profile *prf, int alphabet_size, int *gap_list, int *gap_list_length, int *num_gaps);

void write_iterated_aln(char* old_aln_file_name, char* new_aln_file_name, char *gap_file_name, char *seq1, int *gap_list1, int num_gap1, char *seq2, int *gap_list2, int num_gap2);
