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/*
kalign2_profile_alignment.h
Released under GPL - see the 'COPYING' file
Copyright (C) 2006 Timo Lassmann <timolassmann@gmail.com>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Please send bug reports, comments etc. to:
timolassmann@gmail.com
*/
int local_numseq;
int local_numprofiles;
int* assign_gap_codes(int* seq,int len);
int is_member(struct alignment* aln,int test);
float** dna_profile_distance(struct alignment* aln,float** dm,struct parameters* param, int nj);
float** protein_profile_wu_distance(struct alignment* aln,float** dm,struct parameters* param, int nj);
int** hirschberg_profile_alignment(struct alignment* aln,int* tree,float**submatrix, int** map);
float* make_profile_from_alignment(float* prof, int num,struct alignment* aln,float** subm);
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