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kalign2_hirschberg_large.h

/*
      kalign2_hirschberg_large.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
*/

00026 struct large_states{
      float a;
      float ga;
      float gb;
      float x;
};



00035 struct hirsch_large_mem{
      struct large_states* f;
      struct large_states* b;
      int starta;
      int startb;
      int enda;
      int endb;
      int size;
      int len_a;
      int len_b;
};

int* hirsch_large_pp_dyn(const float* prof1,const float* prof2,struct hirsch_large_mem* hm, int* hirsch_path);
struct large_states* foward_large_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_large_mem* hm);
struct large_states* backward_large_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_large_mem* hm);
int* hirsch_large_align_two_pp_vector(const float* prof1,const float* prof2,struct hirsch_large_mem* hm,int* hirsch_path,float input_states[],int old_cor[]);

int* hirsch_large_ps_dyn(const float* prof1,const int* seq2,struct hirsch_large_mem* hm, int* hirsch_path,int sip);
struct large_states* foward_large_hirsch_ps_dyn(const float* prof1,const int* seq2,struct hirsch_large_mem* hm,int sip);
struct large_states* backward_large_hirsch_ps_dyn(const float* prof1,const int* seq2,struct hirsch_large_mem* hm,int sip);
int* hirsch_large_align_two_ps_vector(const float* prof1,const int* seq2,struct hirsch_large_mem* hm,int* hirsch_path,float input_states[],int old_cor[],int sip);


int* hirsch_large_ss_dyn(float**subm, const int* seq1,const int* seq2,struct hirsch_large_mem* hm, int* hirsch_path);
struct large_states* foward_large_hirsch_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_large_mem* hm);
struct large_states* backward_large_hirsch_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_large_mem* hm);
int* hirsch_large_align_two_ss_vector(float**subm,const int* seq1,const int* seq2,struct hirsch_large_mem* hm,int* hirsch_path,float input_states[],int old_cor[]);

float* make_large_profile(float* prof, int* seq,int len,float** subm);
void set_large_gap_penalties(float* prof,int len,int nsip);
float* large_update(float* profa,float* profb,float* newp,int* path,int sipa,int sipb);

struct hirsch_large_mem* hirsch_large_mem_alloc(struct hirsch_large_mem* hm,int x);
struct hirsch_large_mem* hirsch_large_mem_realloc(struct hirsch_large_mem* hm,int x);
void hirsch_large_mem_free(struct hirsch_large_mem* hm);



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