/* kalign2_advanced_gaps.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 */ void advanced_smooth_gaps(float* prof,int len,int window,float strength); float* advanced_make_profile(float* prof, int* seq,int len,float** subm); float* advanced_update(const float* profa,const float* profb,float* newp,int* path,int sipa,int sipb,float internal_gap_weight); int* advanced_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm, int* hirsch_path); int* advanced_hirsch_align_two_pp_vector(const float* prof1,const float* prof2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[]); struct states* advanced_foward_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm); struct states* advanced_backward_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm);

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