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Viewing changes to t_coffee_source/fastal/iteration.h

  • Committer: Package Import Robot
  • Author(s): Charles Plessy
  • Date: 2013-11-27 21:37:22 UTC
  • mfrom: (1.3.8)
  • Revision ID: package-import@ubuntu.com-20131127213722-q4ujohi94316jrd5
Tags: 10.00.r1613-1
New upstream release.

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t_coffee_source/fastal/iteration.h
 
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/******************************COPYRIGHT NOTICE*******************************/
 
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/*  (c) Centro de Regulacio Genomica                                                        */
 
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/*  and                                                                                     */
 
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/*  Cedric Notredame                                                                        */
 
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/*  22 Oct 2013 - 15:51.                                                                    */
 
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/*All rights reserved.                                                                      */
 
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/*This file is part of T-COFFEE.                                                            */
 
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/*                                                                                          */
 
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/*    T-COFFEE is free software; you can redistribute it and/or modify                      */
 
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/*    it under the terms of the GNU General Public License as published by                  */
 
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/*    the Free Software Foundation; either version 2 of the License, or                     */
 
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/*    (at your option) any later version.                                                   */
 
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/*                                                                                          */
 
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/*    T-COFFEE is distributed in the hope that it will be useful,                           */
 
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/*    but WITHOUT ANY WARRANTY; without even the implied warranty of                        */
 
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/*    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                         */
 
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/*    GNU General Public License for more details.                                          */
 
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/*                                                                                          */
 
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/*    You should have received a copy of the GNU General Public License                     */
 
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/*    along with Foobar; if not, write to the Free Software                                 */
 
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/*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
 
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/*...............................................                                           */
 
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/*  If you need some more information                                                       */
 
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/*  cedric.notredame@europe.com                                                             */
 
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/*...............................................                                           */
 
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/******************************COPYRIGHT NOTICE*******************************/
 
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void seq2profile2(char *seq, Fastal_profile *prf, int *char2pos);
 
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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);
 
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void iterate(Fastal_param *param, void *method_arguments_p, char *aln_file_name, char *out_file_name, int iteration_number);
 
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void edit2seq_pattern(FILE *edit_file, char *seq1, char *seq2);
 
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int *del_gap_from_profile(Fastal_profile *prf, int alphabet_size, int *gap_list, int *gap_list_length, int *num_gaps);
 
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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);