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/*

        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

*/

 

struct large_states{

        float a;

        float ga;

        float gb;

        float x;

};

 

 

 

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);