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kalignP_hirschberg.h
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/*
kalignP_hirschberg.h
Copyright (C) 2010 Nanjiang Shu <nanjiang@sbc.su.se>
Department of Biochemistry and Biophysics
Stockholm University
Description: multiple sequence alignment supporting external supplied
position specific gap penalties
This software is derived from
Kalign version 2.03, Copyright (C) 2006 Timo Lassmann
http://msa.cgb.ki.se/
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
A copy of this license is in the COPYING file.
*/
/* ==== consensus - consensus alignemnt */
int* hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm, int* hirsch_path);
int* hirsch_pp_dyn_new(const float* prof1,const float* prof2,struct hirsch_mem* hm, int* hirsch_path);
int* hirsch_pp_dyn_new0(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2, float* weightArray1, float* weightArray2, struct hirsch_mem* hm, int* hirsch_path);
int* hirsch_pp_dyn_new2(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2, float* weightArray1, float* weightArray2, struct hirsch_mem* hm, int* hirsch_path);
int* hirsch_pp_dyn_new2_test1(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2, float* weightArray1, float* weightArray2, struct hirsch_mem* hm, int* hirsch_path);
int* hirsch_pp_dyn_new2_test2(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2, unsigned int nsip1, unsigned int nsip2, float* weightArray1, float* weightArray2, struct hirsch_mem* hm, int* hirsch_path);
struct states* foward_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm);
struct states* foward_hirsch_pp_dyn_new(const float* prof1,const float* prof2,struct hirsch_mem* hm);
struct states* foward_hirsch_pp_dyn_new0(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,float* weightArray1, float* weightArray2, struct hirsch_mem* hm);
struct states* foward_hirsch_pp_dyn_new2(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,float* weightArray1, float* weightArray2, struct hirsch_mem* hm);
struct states* foward_hirsch_pp_dyn_new2_test1(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,float* weightArray1, float* weightArray2, struct hirsch_mem* hm);
struct states* foward_hirsch_pp_dyn_new2_test2(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,unsigned int nsip1, unsigned int nsip2, float* weightArray1, float* weightArray2, struct hirsch_mem* hm);
struct states* backward_hirsch_pp_dyn(const float* prof1,const float* prof2,struct hirsch_mem* hm);
struct states* backward_hirsch_pp_dyn_new(const float* prof1,const float* prof2,struct hirsch_mem* hm);
struct states* backward_hirsch_pp_dyn_new0(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,float* weightArray1, float* weightArray2, struct hirsch_mem* hm);
struct states* backward_hirsch_pp_dyn_new2(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,float* weightArray1, float* weightArray2, struct hirsch_mem* hm);
struct states* backward_hirsch_pp_dyn_new2_test1(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,float* weightArray1, float* weightArray2, struct hirsch_mem* hm);
struct states* backward_hirsch_pp_dyn_new2_test2(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,unsigned int nsip1, unsigned int nsip2, float* weightArray1, float* weightArray2, struct hirsch_mem* hm);
int* hirsch_align_two_pp_vector(const float* prof1,const float* prof2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[]);
int* hirsch_align_two_pp_vector_new(const float* prof1,const float* prof2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[]);
int* hirsch_align_two_pp_vector_new0(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,float* weightArray1, float* weightArray2, struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[]);
int* hirsch_align_two_pp_vector_new2(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,float* weightArray1, float* weightArray2, struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[]);
int* hirsch_align_two_pp_vector_new2_test1(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,float* weightArray1, float* weightArray2, struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[]);
int* hirsch_align_two_pp_vector_new2_test2(const float* prof1,const float* prof2,unsigned int* nResArray1, unsigned int* nResArray2,unsigned int nsip1, unsigned int nsip2, float* weightArray1, float* weightArray2, struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[]);
struct states* backward_hirsch_pp_dynm(const float* prof1,const float* prof2,struct hirsch_mem* hm);
struct states* backward_hirsch_pp_dyn0(const float* prof1,const float* prof2,struct hirsch_mem* hm);
/* ==== consensus - sequence alignemnt */
int* hirsch_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm, int* hirsch_path,int sip);
int* hirsch_ps_dyn_new(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm, int* hirsch_path,int sip);
int* hirsch_ps_dyn_new0(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm, int* hirsch_path,int sip);
int* hirsch_ps_dyn_new1(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm, int* hirsch_path,unsigned int* nResArray1, int sip);
int* hirsch_ps_dyn_new2(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm, int* hirsch_path,unsigned int* nResArray1, float* weightArray1, int sip);
int* hirsch_ps_dyn_new2_test1(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm, int* hirsch_path,unsigned int* nResArray1, float* weightArray1, int sip);
int* hirsch_ps_dyn_new2_test2(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm, int* hirsch_path,unsigned int* nResArray1, float* weightArray1, int sip);
struct states* foward_hirsch_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm,int sip);
struct states* foward_hirsch_ps_dyn_new(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int sip);
struct states* foward_hirsch_ps_dyn_new0(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int sip);
struct states* foward_hirsch_ps_dyn_new1(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,unsigned int* nResArray1, int sip);
struct states* foward_hirsch_ps_dyn_new2(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,unsigned int* nResArray1, float* weightArray1, int sip);
struct states* foward_hirsch_ps_dyn_new2_test1(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,unsigned int* nResArray1, float* weightArray1, int sip);
struct states* foward_hirsch_ps_dyn_new2_test2(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,unsigned int* nResArray1, float* weightArray1, int sip);
struct states* backward_hirsch_ps_dyn(const float* prof1,const int* seq2,struct hirsch_mem* hm,int sip);
struct states* backward_hirsch_ps_dyn_new(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int sip);
struct states* backward_hirsch_ps_dyn_new0(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int sip);
struct states* backward_hirsch_ps_dyn_new1(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,unsigned int* nResArray1, int sip);
struct states* backward_hirsch_ps_dyn_new2(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,unsigned int* nResArray1, float* weightArray1, int sip);
struct states* backward_hirsch_ps_dyn_new2_test1(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,unsigned int* nResArray1, float* weightArray1, int sip);
struct states* backward_hirsch_ps_dyn_new2_test2(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,unsigned int* nResArray1, float* weightArray1, int sip);
int* hirsch_align_two_ps_vector(const float* prof1,const int* seq2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[],int sip);
int* hirsch_align_two_ps_vector_new(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[],int sip);
int* hirsch_align_two_ps_vector_new0(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[],int sip);
int* hirsch_align_two_ps_vector_new1(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[],unsigned int* nResArray1, int sip);
int* hirsch_align_two_ps_vector_new2(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[],unsigned int* nResArray1, float* weightArray1, int sip);
int* hirsch_align_two_ps_vector_new2_test1(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[],unsigned int* nResArray1, float* weightArray1, int sip);
int* hirsch_align_two_ps_vector_new2_test2(const float* prof1,const int* seq2,const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2,struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[],unsigned int* nResArray1, float* weightArray1, int sip);
/* ==== sequence - sequence alignemnt */
int* hirsch_ss_dyn(float**subm, const int* seq1,const int* seq2,struct hirsch_mem* hm, int* hirsch_path);
int* hirsch_ss_dyn_new(float**subm, const int* seq1,const int* seq2,const float* gpoArray1, const float*gpeArray1, const float* tgpeArray1, const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm, int* hirsch_path);
struct states* foward_hirsch_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_mem* hm);
struct states* foward_hirsch_ss_dyn_new(float**subm,const int* seq1,const int* seq2,const float* gpoArray1, const float*gpeArray1, const float* tgpeArray1, const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm);
struct states* backward_hirsch_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_mem* hm);
struct states* backward_hirsch_ss_dyn_new(float**subm,const int* seq1,const int* seq2,const float* gpoArray1, const float*gpeArray1, const float* tgpeArray1, const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm);
int* hirsch_align_two_ss_vector(float**subm,const int* seq1,const int* seq2, struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[]);
int* hirsch_align_two_ss_vector_new(float**subm,const int* seq1,const int* seq2,const float* gpoArray1, const float*gpeArray1, const float* tgpeArray1, const float* gpoArray2, const float* gpeArray2, const float* tgpeArray2, struct hirsch_mem* hm,int* hirsch_path,float input_states[],int old_cor[]);