-
Notifications
You must be signed in to change notification settings - Fork 0
/
kalignP_hirschberg_large.h
78 lines (59 loc) · 3.3 KB
/
kalignP_hirschberg_large.h
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
/*
kalignP_hirschberg_large.h
Copyright (C) 2010 Nanjiang Shu <[email protected]>
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/
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.
*/
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);