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kalignP_hirschberg_large.c
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kalignP_hirschberg_large.c
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/*
kalignP_hirschberg_large.c
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.
*/
#include "kalignP.h"
#include "kalignP_hirschberg_large.h"
#define MAX(a, b) (a > b ? a : b)
#define MAX3(a,b,c) MAX(MAX(a,b),c)
//#include <emmintrin.h>
float local_gpo;
float local_gpe;
float local_tgpe;
int** hirschberg_large_alignment(struct alignment* aln,int* tree,float**submatrix, int** map,int window,float strength)
{
struct hirsch_large_mem* hm = 0;
int i,j,g,a,b,c;
int len_a;
int len_b;
float** profile = 0;
float** subm = 0;
subm = malloc(sizeof(float*)*32);
for(i = 0; i < 32;i++){
subm[i] = malloc(sizeof(float)*32);
for (j = 0; j < 32;j++){
subm[i][j] = (float)submatrix[i][j];
}
}
local_gpo = (float)gpo;
local_gpe = (float)gpe;
local_tgpe = (float)tgpe;
profile = malloc(sizeof(float*)*numprofiles);
for ( i = 0;i< numprofiles;i++){
profile[i] = 0;
}
map = malloc(sizeof(int*)*numprofiles);
for ( i = 0;i < numprofiles;i++){
map[i] = 0;
}
hm = hirsch_large_mem_alloc(hm,1024);
fprintf(stderr,"\nAlignment:\n");
for (i = 0; i < (numseq-1);i++){
a = tree[i*3];
b = tree[i*3+1];
c = tree[i*3+2];
fprintf(stderr,"\r%8.0f percent done",(float)(i) /(float)numseq * 100);
//fprintf(stderr,"Aligning:%d %d->%d done:%f\n",a,b,c,((float)(i+1)/(float)numseq)*100);
len_a = aln->sl[a];
len_b = aln->sl[b];
g = (len_a > len_b)? len_a:len_b;
map[c] = malloc(sizeof(int) * (g+2));
if(g > hm->size){
hm = hirsch_large_mem_realloc(hm,g);
}
for (j = 0; j < (g+2);j++){
map[c][j] = -1;
}
if (a < numseq){
profile[a] = make_large_profile(profile[a],aln->s[a],len_a,subm);
}else{
set_large_gap_penalties(profile[a],len_a,aln->nsip[b]);
}
if (b < numseq){
profile[b] = make_large_profile(profile[b],aln->s[b],len_b,subm);
}else{
set_large_gap_penalties(profile[b],len_b,aln->nsip[a]);
}
hm->starta = 0;
hm->startb = 0;
hm->enda = len_a;
hm->endb = len_b;
hm->len_a = len_a;
hm->len_b = len_b;
hm->f[0].a = 0.0;
hm->f[0].ga = -FLOATINFTY;
hm->f[0].gb = -FLOATINFTY;
hm->b[0].a = 0.0;
hm->b[0].ga = -FLOATINFTY;
hm->b[0].gb = -FLOATINFTY;
// fprintf(stderr,"LENA:%d LENB:%d numseq:%d\n",len_a,len_b,numseq);
if(a < numseq){
if(b < numseq){
map[c] = hirsch_large_ss_dyn(subm,aln->s[a],aln->s[b],hm,map[c]);
}else{
hm->enda = len_b;
hm->endb = len_a;
hm->len_a = len_b;
hm->len_b = len_a;
map[c] = hirsch_large_ps_dyn(profile[b],aln->s[a],hm,map[c],aln->nsip[b]);
map[c] = mirror_hirsch_path(map[c],len_a,len_b);
}
}else{
if(b < numseq){
map[c] = hirsch_large_ps_dyn(profile[a],aln->s[b],hm,map[c],aln->nsip[a]);
}else{
if(len_a < len_b){
map[c] = hirsch_large_pp_dyn(profile[a],profile[b],hm,map[c]);
}else{
hm->enda = len_b;
hm->endb = len_a;
hm->len_a = len_b;
hm->len_b = len_a;
map[c] = hirsch_large_pp_dyn(profile[b],profile[a],hm,map[c]);
map[c] = mirror_hirsch_path(map[c],len_a,len_b);
}
}
}
map[c] = add_gap_info_to_hirsch_path(map[c],len_a,len_b);
if(i != numseq-2){
profile[c] = malloc(sizeof(float)*64*(map[c][0]+2));
profile[c] = large_update(profile[a],profile[b],profile[c],map[c],aln->nsip[a],aln->nsip[b]);
}
aln->sl[c] = map[c][0];
aln->nsip[c] = aln->nsip[a] + aln->nsip[b];
aln->sip[c] = malloc(sizeof(int)*(aln->nsip[a] + aln->nsip[b]));
g =0;
for (j = aln->nsip[a];j--;){
aln->sip[c][g] = aln->sip[a][j];
g++;
}
for (j = aln->nsip[b];j--;){
aln->sip[c][g] = aln->sip[b][j];
g++;
}
free(profile[a]);
free(profile[b]);
}
fprintf(stderr,"\r%8.0f percent done\n",100.0);
free(profile);
hirsch_large_mem_free(hm);
for (i = 32;i--;){
free(subm[i]);
free(submatrix[i]);
}
free(subm);
free(submatrix);
return map;
}
int* hirsch_large_ss_dyn(float**subm, const int* seq1,const int* seq2,struct hirsch_large_mem* hm, int* hirsch_path)
{
int mid = ((hm->enda - hm->starta) / 2)+ hm->starta;
float input_states[6] = {hm->f[0].a,hm->f[0].ga,hm->f[0].gb,hm->b[0].a,hm->b[0].ga,hm->b[0].gb};
int old_cor[5] = {hm->starta,hm->enda,hm->startb,hm->endb,mid};
if(hm->starta >= hm->enda){
return hirsch_path;
}
if(hm->startb >= hm->endb){
return hirsch_path;
}
hm->enda = mid;
//fprintf(stderr,"Forward:%d-%d %d-%d\n",hm->starta,hm->enda,hm->startb,hm->endb);
hm->f = foward_large_hirsch_ss_dyn(subm,seq1,seq2,hm);
hm->starta = mid;
hm->enda = old_cor[1];
//fprintf(stderr,"Backward:%d-%d %d-%d\n",hm->starta,hm->enda,hm->startb,hm->endb);
hm->b = backward_large_hirsch_ss_dyn(subm,seq1,seq2,hm);
hirsch_path = hirsch_large_align_two_ss_vector(subm,seq1,seq2,hm,hirsch_path,input_states,old_cor);
return hirsch_path;
}
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[])
{
struct large_states* f = hm->f;
struct large_states* b = hm->b;
int i,j,c;
int transition = -1;
//code:
// a -> a = 1
// a -> ga = 2
// a -> gb = 3
// ga ->ga = 4
// ga -> a = 5
//gb->gb = 6;
//gb->a = 7;
//int max = -FLOATINFTY;
float max = -FLOATINFTY;
//float middle = (hm->endb - hm->startb)/2 + hm->startb;
float middle = (old_cor[3] - old_cor[2])/2 + old_cor[2];
float sub = 0.0;
//i = hm->startb;
i = old_cor[2];
c = -1;
//for(i = hm->startb; i < hm->endb;i++){
for(i = old_cor[2]; i < old_cor[3];i++){
sub = abs(middle -i);
sub /= 1000;
// fprintf(stderr,"%d-%d %f\n",hm->startb,hm->endb,sub);
if(f[i].a+b[i].a-sub > max){
max = f[i].a+b[i].a-sub;
// fprintf(stderr,"aligned->aligned:%d + %d = %d\n",f[i].a,b[i].a,f[i].a+b[i].a);
transition = 1;
c = i;
}
if(f[i].a+b[i].ga-local_gpo-sub > max){
max = f[i].a+b[i].ga-local_gpo-sub;
// fprintf(stderr,"aligned->gap_a:%d + %d +%d = %d\n",f[i].a,b[i].ga,prof1[27],f[i].a+b[i].ga+prof2[27]);
transition = 2;
c = i;
}
if(f[i].a+b[i].gb -local_gpo -sub > max){
max = f[i].a+b[i].gb - local_gpo-sub;
// fprintf(stderr,"aligned->gap_b:%d + %d +%d = %d\n",f[i].a,b[i].gb,prof1[27],f[i].a+b[i].gb+prof1[27]);
transition = 3;
c = i;
}
if(f[i].ga+b[i].a - local_gpo-sub > max){
max = f[i].ga+b[i].a - local_gpo-sub;
// fprintf(stderr,"gap_a->aligned:%d + %d + %d(local_gpo) = %d\n",f[i].ga,b[i].a,prof2[27],f[i].ga+b[i].a+prof2[27]);
transition = 5;
c = i;
}
if(hm->startb == 0){
if(f[i].gb+b[i].gb - local_tgpe-sub > max){
max = f[i].gb+b[i].gb -local_tgpe-sub;
// fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
transition = 6;
c = i;
}
}else{
if(f[i].gb+b[i].gb - local_gpe -sub> max){
max = f[i].gb+b[i].gb - local_gpe-sub;
// fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
transition = 6;
c = i;
}
}
if(f[i].gb+b[i].a - local_gpo-sub > max){
max = f[i].gb+b[i].a - local_gpo-sub;
// fprintf(stderr,"gap_b->aligned:%d + %d + %d(local_gpo) = %d\n",f[i].gb,b[i].a,prof1[27],f[i].gb+b[i].a+prof1[27]);
transition = 7;
c = i;
}
}
//i = hm->endb;
i = old_cor[3];
sub = abs(middle -i);
sub /= 1000;
if(f[i].a+b[i].gb-local_gpo-sub > max){
max = f[i].a+b[i].gb - local_gpo-sub;
// fprintf(stderr,"aligned->gap_b:%d + %d +%d = %d\n",f[i].a,b[i].gb,prof1[27],f[i].a+b[i].gb+prof1[27]);
transition = 3;
c = i;
}
if(hm->endb == hm->len_b){
if(f[i].gb+b[i].gb -local_tgpe-sub > max){
max = f[i].gb+b[i].gb - local_tgpe-sub;
// fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
transition = 6;
c = i;
}
}else{
if(f[i].gb+b[i].gb - gpe-sub > max){
max = f[i].gb+b[i].gb - gpe-sub;
// fprintf(stderr,"gap_b->gap_b:%d + %d +%d(local_gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
transition = 6;
c = i;
}
}
//fprintf(stderr,"Transition:%d at:%d\n",transition,c);
j = hirsch_path[0];
switch(transition){
case 1: //a -> a = 1
hirsch_path[old_cor[4]] = c;
hirsch_path[old_cor[4]+1] = c+1;
// fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);
// fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);
//foward:
hm->f[0].a = input_states[0];
hm->f[0].ga = input_states[1];
hm->f[0].gb = input_states[2];
hm->b[0].a = 0;
hm->b[0].ga = -FLOATINFTY;
hm->b[0].gb = -FLOATINFTY;
// fprintf(stderr,"Using this for start:%d %d %d\n",hm->f[0].a,hm->f[0].ga,hm->f[0].gb);
hm->starta = old_cor[0];
hm->enda = old_cor[4]-1;
hm->startb = old_cor[2];
hm->endb = c-1;
//fprintf(stderr,"Following first: %d what:%d-%d %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
hirsch_path = hirsch_large_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
//backward:
hm->starta = old_cor[4]+1;
hm->enda = old_cor[1];
hm->startb = c+1;
hm->endb = old_cor[3];
hm->f[0].a = 0;
hm->f[0].ga = -FLOATINFTY;
hm->f[0].gb = -FLOATINFTY;
hm->b[0].a = input_states[3];
hm->b[0].ga = input_states[4];
hm->b[0].gb = input_states[5];
//fprintf(stderr,"Following last: %d what:%d-%d %d-%d\n",c+1,hm->starta,hm->enda,hm->startb,hm->endb);
hirsch_path = hirsch_large_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
break;
case 2:// a -> ga = 2
hirsch_path[old_cor[4]] = c;
// fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);
//foward:
hm->f[0].a = input_states[0];
hm->f[0].ga = input_states[1];
hm->f[0].gb = input_states[2];
hm->b[0].a = 0;
hm->b[0].ga = -FLOATINFTY;
hm->b[0].gb = -FLOATINFTY;
hm->starta = old_cor[0];
hm->enda = old_cor[4]-1;
hm->startb = old_cor[2];
hm->endb = c-1;
//fprintf(stderr,"Following first: %d what:%d-%d %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
hirsch_path = hirsch_large_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
//backward:
hm->starta = old_cor[4];
hm->enda = old_cor[1];
hm->startb = c+1;
hm->endb = old_cor[3];
hm->f[0].a = -FLOATINFTY;
hm->f[0].ga = 0;
hm->f[0].gb = -FLOATINFTY;
hm->b[0].a = input_states[3];
hm->b[0].ga = input_states[4];
hm->b[0].gb = input_states[5];
//fprintf(stderr,"Following last: %d what:%d-%d %d-%d\n",c+1,hm->starta,hm->enda,hm->startb,hm->endb);
hirsch_path = hirsch_large_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
break;
case 3:// a -> gb = 3
hirsch_path[old_cor[4]] = c;
// fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);
//foward:
hm->f[0].a = input_states[0];
hm->f[0].ga = input_states[1];
hm->f[0].gb = input_states[2];
hm->b[0].a = 0;
hm->b[0].ga = -FLOATINFTY;
hm->b[0].gb = -FLOATINFTY;
hm->starta = old_cor[0];
hm->enda = old_cor[4]-1;
hm->startb = old_cor[2];
hm->endb = c-1;
//fprintf(stderr,"Following first: %d what:%d-%d %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
hirsch_path = hirsch_large_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
//backward:
hm->starta = old_cor[4]+1;
hm->enda = old_cor[1];
hm->startb = c;
hm->endb = old_cor[3];
hm->f[0].a = -FLOATINFTY;
hm->f[0].ga = -FLOATINFTY;
hm->f[0].gb = 0;
hm->b[0].a = input_states[3];
hm->b[0].ga = input_states[4];
hm->b[0].gb = input_states[5];
//fprintf(stderr,"Following last: %d\n",c+1);
hirsch_path = hirsch_large_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
break;
case 5://ga -> a = 5
hirsch_path[old_cor[4]+1] = c+1;
// fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);
//foward:
hm->f[0].a = input_states[0];
hm->f[0].ga = input_states[1];
hm->f[0].gb = input_states[2];
hm->b[0].a = -FLOATINFTY;
hm->b[0].ga = 0;
hm->b[0].gb = -FLOATINFTY;
hm->starta = old_cor[0];
hm->enda = old_cor[4];
hm->startb = old_cor[2];
hm->endb = c-1;
//fprintf(stderr,"Following first: %d what:%d-%d %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
hirsch_path = hirsch_large_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
//backward:
hm->starta = old_cor[4]+1;
hm->enda = old_cor[1];
hm->startb = c+1;
hm->endb = old_cor[3];
hm->f[0].a = 0;
hm->f[0].ga = -FLOATINFTY;
hm->f[0].gb = -FLOATINFTY;
hm->b[0].a = input_states[3];
hm->b[0].ga = input_states[4];
hm->b[0].gb = input_states[5];
//fprintf(stderr,"Following last: %d\n",c+1);
hirsch_path = hirsch_large_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
break;
case 6://gb->gb = 6;
//foward:
hm->f[0].a = input_states[0];
hm->f[0].ga = input_states[1];
hm->f[0].gb = input_states[2];
hm->b[0].a = -FLOATINFTY;
hm->b[0].ga = -FLOATINFTY;
hm->b[0].gb = 0;
hm->starta = old_cor[0];
hm->enda = old_cor[4]-1;
hm->startb = old_cor[2];
hm->endb = c;
//fprintf(stderr,"Following first: %d what:%d-%d %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
hirsch_path = hirsch_large_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
//backward:
hm->starta = old_cor[4]+1;
hm->enda = old_cor[1];
hm->startb = c;
hm->endb = old_cor[3];
hm->f[0].a = -FLOATINFTY;
hm->f[0].ga = -FLOATINFTY;
hm->f[0].gb = 0;
hm->b[0].a = input_states[3];
hm->b[0].ga = input_states[4];
hm->b[0].gb = input_states[5];
//fprintf(stderr,"Following last: %d\n",c+1);
hirsch_path = hirsch_large_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
break;
case 7://gb->a = 7;
hirsch_path[old_cor[4]+1] = c+1;
// fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);
//foward:
hm->f[0].a = input_states[0];
hm->f[0].ga = input_states[1];
hm->f[0].gb = input_states[2];
hm->b[0].a = -FLOATINFTY;
hm->b[0].ga = -FLOATINFTY;
hm->b[0].gb = 0;
hm->starta = old_cor[0];
hm->enda = old_cor[4]-1;
hm->startb = old_cor[2];
hm->endb = c;
//fprintf(stderr,"Following first: %d what:%d-%d %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
hirsch_path = hirsch_large_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
//backward:
hm->starta = old_cor[4]+1;
hm->enda = old_cor[1];
hm->startb = c+1;
hm->endb = old_cor[3];
hm->f[0].a = 0;
hm->f[0].ga = -FLOATINFTY;
hm->f[0].gb = -FLOATINFTY;
hm->b[0].a = input_states[3];
hm->b[0].ga = input_states[4];
hm->b[0].gb = input_states[5];
//fprintf(stderr,"Following last: %d\n",c+1);
hirsch_path = hirsch_large_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
break;
}
return 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* s = hm->f;
float *subp = 0;
const int starta = hm->starta;
const int enda = hm->enda;
const int startb = hm->startb;
const int endb = hm->endb;
register float pa = 0;
register float pga = 0;
register float pgb = 0;
register float ca = 0;
register int i = 0;
register int j = 0;
s[startb].a = s[0].a;
s[startb].ga = s[0].ga;
s[startb].gb = s[0].gb;
if(startb == 0){
for (j = startb+1; j < endb;j++){
s[j].a = -FLOATINFTY;
//s[j].ga = s[j-1].a-local_tgpe;
//if (s[j-1].ga-local_tgpe > s[j].ga){
// s[j].ga = s[j-1].ga-local_tgpe;
//}
//if(s[j-1].ga > s[j-1].a){
// s[j].ga = s[j-1].ga-local_tgpe;
//}else{
// s[j].ga = s[j-1].a-local_tgpe;
//}
s[j].ga = MAX(s[j-1].ga,s[j-1].a)-local_tgpe;
s[j].gb = -FLOATINFTY;
}
}else{
for (j = startb+1; j < endb;j++){
s[j].a = -FLOATINFTY;
//s[j].ga = s[j-1].a-local_gpo;
//if (s[j-1].ga - gpe > s[j].ga){
// s[j].ga = s[j-1].ga-gpe;
//}
//if(s[j-1].ga - gpe >s[j-1].a-local_gpo){
// s[j].ga = s[j-1].ga-gpe;
//}else{
// s[j].ga = s[j-1].a-local_gpo;
//}
s[j].ga = MAX(s[j-1].ga - local_gpe,s[j-1].a-local_gpo);
s[j].gb = -FLOATINFTY;
}
}
s[endb].a = -FLOATINFTY;
s[endb].ga = -FLOATINFTY;
s[endb].gb = -FLOATINFTY;
seq2--;
for (i = starta;i < enda;i++){
subp = subm[seq1[i]];
pa = s[startb].a;
pga = s[startb].ga;
pgb = s[startb].gb;
if(startb == 0){
s[startb].a = -FLOATINFTY;
s[startb].ga = -FLOATINFTY;
//s[startb].gb = pa-local_tgpe;
//if(pgb - local_tgpe > s[startb].gb){
// s[startb].gb = pgb-local_tgpe;
//}
//if(pgb > pa){
// s[startb].gb = pgb-local_tgpe;
//}else{
// s[startb].gb = pa-local_tgpe;
//}
s[startb].gb = MAX(pgb,pa) - local_tgpe;
}else{
s[startb].a = -FLOATINFTY;
s[startb].ga = -FLOATINFTY;
//s[startb].gb = pa-local_gpo;
//if(pgb -gpe > s[startb].gb){
// s[startb].gb = pgb -gpe;
//}
//if(pgb - gpe > pa - local_gpo){
// s[startb].gb = pgb - gpe;
//}else{
// s[startb].gb = pa - local_gpo;
//}
s[startb].gb = MAX(pgb - local_gpe,pa - local_gpo);
}
for (j = startb+1; j <= endb;j++){
ca = s[j].a;
//if((pga -= local_gpo) > pa){
// pa = pga;
//}
//if((pgb -= local_gpo) > pa){
// pa = pgb;
//}
pa = MAX3(pa,pga-local_gpo,pgb-local_gpo);
pa += subp[seq2[j]];
s[j].a = pa;
pga = s[j].ga;
//s[j].ga = s[j-1].a-local_gpo;
//if (s[j-1].ga-gpe > s[j].ga){
// s[j].ga = s[j-1].ga-gpe;
//}
//if(s[j-1].ga-gpe >s[j-1].a-local_gpo){
// s[j].ga = s[j-1].ga-gpe;
//}else{
// s[j].ga = s[j-1].a-local_gpo;
//}
s[j].ga = MAX(s[j-1].ga-local_gpe,s[j-1].a-local_gpo);
pgb = s[j].gb;
//s[j].gb = ca-local_gpo;
//if(pgb-gpe > s[j].gb){
// s[j].gb = pgb-gpe;
//}
//if(pgb-gpe > ca-local_gpo){
// s[j].gb = pgb-gpe;
//}else{
// s[j].gb = ca-local_gpo;
//}
s[j].gb = MAX(pgb-local_gpe ,ca-local_gpo);
pa = ca;
}
}
return s;
}
struct large_states* backward_large_hirsch_ss_dyn(float**subm,const int* seq1,const int* seq2,struct hirsch_large_mem* hm)
{
struct large_states* s = hm->b;
float *subp = 0;
const int starta = hm->starta;
const int enda = hm->enda;
const int startb = hm->startb;
const int endb = hm->endb;
register float pa = 0;
register float pga = 0;
register float pgb = 0;
register float ca = 0;
register int i = 0;
register int j = 0;
s[endb].a = s[0].a ;
s[endb].ga = s[0].ga;
s[endb].gb = s[0].gb;
//init of first row;
//j = endb-startb;
if(endb == hm->len_b){
for(j = endb-1;j > startb;j--){
s[j].a = -FLOATINFTY;
//s[j].ga = s[j+1].a-local_tgpe;
//if (s[j+1].ga-local_tgpe > s[j].ga){
// s[j].ga = s[j+1].ga-local_tgpe;
//}
//if(s[j+1].ga > s[j+1].a){
// s[j].ga = s[j+1].ga-local_tgpe;
//}else{
// s[j].ga = s[j+1].a-local_tgpe;
//}
s[j].ga = MAX(s[j+1].ga,s[j+1].a)-local_tgpe;
s[j].gb = -FLOATINFTY;
}
}else{
for(j = endb-1;j > startb;j--){
s[j].a = -FLOATINFTY;
//s[j].ga = s[j+1].a-local_gpo;
//if (s[j+1].ga-gpe > s[j].ga){
// s[j].ga = s[j+1].ga-gpe;
//}
//if(s[j+1].ga-gpe > s[j+1].a-local_gpo){
// s[j].ga = s[j+1].ga-gpe;
//}else{
// s[j].ga = s[j+1].a-local_gpo;
//}
s[j].ga = MAX(s[j+1].ga-local_gpe,s[j+1].a-local_gpo);
s[j].gb = -FLOATINFTY;
}
}
s[startb].a = -FLOATINFTY;
s[startb].ga = -FLOATINFTY;
s[startb].gb = -FLOATINFTY;
i = enda-starta;
seq1+= starta;
while(i--){
subp = subm[seq1[i]];
pa = s[endb].a;
pga = s[endb].ga;
pgb = s[endb].gb;
s[endb].a = -FLOATINFTY;
s[endb].ga = -FLOATINFTY;
if(endb == hm->len_b){
//s[endb].gb = pa-local_tgpe;
//if(pgb-local_tgpe > s[endb].gb){
// s[endb].gb = pgb-local_tgpe;
//}
//if(pgb > pa){
// s[endb].gb = pgb-local_tgpe;
//}else{
// s[endb].gb = pa-local_tgpe;
//}
s[endb].gb = MAX(pgb,pa)-local_tgpe;
}else{
//s[endb].gb = pa-local_gpo;
//if(pgb-gpe > s[endb].gb){
// s[endb].gb = pgb-gpe;
//}
//if(pgb-gpe > pa-local_gpo){
// s[endb].gb = pgb-gpe;
//}else{
// s[endb].gb = pa-local_gpo;
//}
s[endb].gb = MAX(pgb-local_gpe,pa-local_gpo);
}
for(j = endb-1;j >= startb;j--){
ca = s[j].a;
//if((pga -= local_gpo) > pa){
// pa = pga;
//}
//if((pgb -= local_gpo) > pa){
// pa = pgb;
//}
pa = MAX3(pa,pga - local_gpo,pgb-local_gpo);
pa += subp[seq2[j]];
s[j].a = pa;
pga = s[j].ga;
//s[j].ga = s[j+1].a-local_gpo;
//if (s[j+1].ga-gpe > s[j].ga){
// s[j].ga = s[j+1].ga-gpe;
//}
//if(s[j+1].ga-gpe >s[j+1].a-local_gpo){
// s[j].ga = s[j+1].ga-gpe;
//}else{
// s[j].ga = s[j+1].a-local_gpo;
//}
s[j].ga = MAX(s[j+1].ga-local_gpe,s[j+1].a-local_gpo);
pgb = s[j].gb;
//s[j].gb = ca-local_gpo;
//if(pgb-gpe > s[j].gb){
// s[j].gb = pgb-gpe;
//}
//if(pgb-gpe > ca-local_gpo){
// s[j].gb = pgb-gpe;
//}else{
// s[j].gb = ca-local_gpo;
//}
s[j].gb = MAX(pgb-local_gpe,ca-local_gpo);
pa = ca;
}
}
return s;
}
int* hirsch_large_ps_dyn(const float* prof1,const int* seq2,struct hirsch_large_mem* hm, int* hirsch_path,int sip)
{
int mid = ((hm->enda - hm->starta) / 2)+ hm->starta;
float input_states[6] = {hm->f[0].a,hm->f[0].ga,hm->f[0].gb,hm->b[0].a,hm->b[0].ga,hm->b[0].gb};
int old_cor[5] = {hm->starta,hm->enda,hm->startb,hm->endb,mid};
if(hm->starta >= hm->enda){
return hirsch_path;
}
if(hm->startb >= hm->endb){
return hirsch_path;
}
hm->enda = mid;
hm->f = foward_large_hirsch_ps_dyn(prof1,seq2,hm,sip);
/*int i;
fprintf(stderr,"FOWARD\n");
for (i = hm->startb; i <= hm->endb;i++){
fprintf(stderr,"%d %d %d\n",hm->f[i].a,hm->f[i].ga,hm->f[i].gb);
}*/
hm->starta = mid;
hm->enda = old_cor[1];
hm->b = backward_large_hirsch_ps_dyn(prof1,seq2,hm,sip);
/*fprintf(stderr,"BaCKWARD\n");
for (i = hm->startb; i <= hm->endb;i++){
fprintf(stderr,"%d %d %d\n",hm->b[i].a,hm->b[i].ga,hm->b[i].gb);
}*/
hirsch_path = hirsch_large_align_two_ps_vector(prof1,seq2,hm,hirsch_path,input_states,old_cor,sip);
return hirsch_path;
}
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)
{
struct large_states* f = hm->f;
struct large_states* b = hm->b;
int i,j,c;
int transition = -1;
const float open = local_gpo * sip;
//code:
// a -> a = 1
// a -> ga = 2
// a -> gb = 3
// ga ->ga = 4
// ga -> a = 5
//gb->gb = 6;
//gb->a = 7;
//int max = -FLOATINFTY;
float max = -FLOATINFTY;
//float middle = (hm->endb - hm->startb)/2 + hm->startb;
float middle = (old_cor[3] - old_cor[2])/2 + old_cor[2];
float sub = 0.0;
prof1+= ((old_cor[4]+1)<<6);
//i = hm->startb;
i = old_cor[2];
c = -1;
//for(i = hm->startb; i < hm->endb;i++){
for(i = old_cor[2]; i < old_cor[3];i++){
sub = abs(middle -i);
sub /= 1000;
if(f[i].a+b[i].a-sub> max){
max = f[i].a+b[i].a-sub;
// fprintf(stderr,"aligned->aligned:%d + %d = %d\n",f[i].a,b[i].a,f[i].a+b[i].a);
transition = 1;
c = i;
}
if(f[i].a+b[i].ga-open-sub > max){
max = f[i].a+b[i].ga-open-sub;
// fprintf(stderr,"aligned->gap_a:%d + %d +%d = %d\n",f[i].a,b[i].ga,prof1[27],f[i].a+b[i].ga+prof2[27]);
transition = 2;
c = i;
}
if(f[i].a+b[i].gb+prof1[27]-sub > max){
max = f[i].a+b[i].gb+prof1[27]-sub;
// fprintf(stderr,"aligned->gap_b:%d + %d +%d = %d\n",f[i].a,b[i].gb,prof1[27],f[i].a+b[i].gb+prof1[27]);
transition = 3;
c = i;
}
if(f[i].ga+b[i].a-open-sub > max){
max = f[i].ga+b[i].a-open-sub;
// fprintf(stderr,"gap_a->aligned:%d + %d + %d(local_gpo) = %d\n",f[i].ga,b[i].a,prof2[27],f[i].ga+b[i].a+prof2[27]);
transition = 5;
c = i;
}
if(hm->startb == 0){
if(f[i].gb+b[i].gb+prof1[29]-sub > max){
max = f[i].gb+b[i].gb+prof1[29]-sub;
// fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
transition = 6;
c = i;
}
}else{
if(f[i].gb+b[i].gb+prof1[28]-sub > max){
max = f[i].gb+b[i].gb+prof1[28]-sub;
// fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
transition = 6;
c = i;
}
}
if(f[i].gb+b[i].a+prof1[27]-sub > max){
max = f[i].gb+b[i].a+prof1[27]-sub;
// fprintf(stderr,"gap_b->aligned:%d + %d + %d(local_gpo) = %d\n",f[i].gb,b[i].a,prof1[27],f[i].gb+b[i].a+prof1[27]);
transition = 7;
c = i;
}
}
//i = hm->endb;
i = old_cor[3];
sub = abs(middle -i);
sub /= 1000;
if(f[i].a+b[i].gb+prof1[27]-sub > max){
max = f[i].a+b[i].gb+prof1[27]-sub;
// fprintf(stderr,"aligned->gap_b:%d + %d +%d = %d\n",f[i].a,b[i].gb,prof1[27],f[i].a+b[i].gb+prof1[27]);
transition = 3;
c = i;
}
if(hm->endb == hm->len_b){
if(f[i].gb+b[i].gb+prof1[29]-sub > max){
max = f[i].gb+b[i].gb+prof1[29]-sub;
// fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
transition = 6;
c = i;
}
}else{
if(f[i].gb+b[i].gb+prof1[28]-sub > max){
max = f[i].gb+b[i].gb+prof1[28]-sub;
// fprintf(stderr,"gap_b->gap_b:%d + %d +%d(gpe) =%d \n",f[i].gb, b[i].gb, prof1[28],f[i].gb+b[i].gb+prof1[28]);
transition = 6;
c = i;
}
}
prof1-= ((old_cor[4]+1)<<6);
//fprintf(stderr,"Transition:%d at:%d\n",transition,c);