/*
	feature.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
*/

#include <string.h>

float* feature_hirschberg_update(const float* profa,const float* profb,float* newp,int* path,int sipa,int sipb);
float* make_unified_profile(float* prof,struct alignment* aln, int num,float** subm,struct feature_matrix* fm);
void set_unified_gap_penalties(float* prof,int len,int nsip);

int* feature_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm, int* hirsch_path);
int* feature_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* feature_foward_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm);
struct states* feature_backward_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm);

