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kalignP_hirschberg.c
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kalignP_hirschberg.c
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/*
kalignP_hirschberg.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.h"
#define MAX(a, b) (a > b ? a : b)
#define MAX3(a,b,c) MAX(MAX(a,b),c)
//#include <emmintrin.h>
int** hirschberg_alignment(struct alignment* aln,int* tree,float**submatrix, int** map,int window,float strength)/*{{{*/
/*strength: param->gap_inc, default = 0.0*/
{
struct hirsch_mem* hm = 0;
int i,j,g,a,b,c;
int len_a;
int len_b;
float** profile = 0;
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;
}
for (i = 0; i < numseq; i ++){ /*set the number of residues at each position of the sequence 2010-10-19 */
aln->nRes[i] = malloc(sizeof(unsigned int) * (aln->sl[i]+2));
for (j = 0; j < aln->sl[i]+2; j ++){
aln->nRes[i][j] = 1;
}
}
hm = hirsch_mem_alloc(hm,1024);/*initially allocated size is 1024, if the max(lena,lenb) is > 1024, it will be re-allocated*/
fprintf(stderr,"\nAlignment:\n");
#ifdef DEBUG/*{{{*/
fprintf(stderr,"Tree:\n");
for (i = 0; i < numseq; i ++)
{
fprintf(stderr,"Tree:%d: %3d %3d %3d\n", i, tree[i*3], tree[i*3+1], tree[i*3+2]);
}
#endif /*}}}*/
float* weightArray_a = 0;
float* weightArray_b = 0;
for (i = 0; i < (numseq-1);i++){
weightArray_a = 0;
weightArray_b = 0;
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);
#ifdef DEBUG/*{{{*/
fprintf(stderr,"\nAligning:%d %d->%d done:%f\n",a,b,c,((float)(i+1)/(float)numseq)*100);
fprintf(stderr,"\ngpo=%f\ngpe=%f\ntgpe=%f\n",gpo,gpe,tgpe);
#endif /*}}}*/
len_a = aln->sl[a];
len_b = aln->sl[b];
g = (len_a > len_b)? len_a:len_b; /*max(len_a, len_b)*/
map[c] = malloc(sizeof(int) * (g+2));
if(g > hm->size){
hm = hirsch_mem_realloc(hm,g);
}
for (j = 0; j < (g+2);j++){
map[c][j] = -1;
}
if (a < numseq){
/*profile[a] = make_profile(profile[a],aln->s[a],len_a,submatrix);*/
profile[a] = make_profile_new(profile[a],aln->s[a],aln->gpo[a], aln->gpe[a], aln->tgpe[a], len_a,submatrix);
}else{ /*set_gap_penalties for consensus sequences, e.g. for A, B, C, E four sequences, when compared (AB) to C, the gap penalties for (AB) should be reset*/
/*set_gap_penalties(profile[a],len_a,aln->nsip[b],strength,aln->nsip[a]);[>this can be modified<]*/
weightArray_a = malloc(sizeof(float)*(len_a+2));
set_gap_penalties_new(profile[a],len_a,aln->nsip[b],strength,aln->nsip[a], weightArray_a);/*this can be modified*/
//smooth_gaps(profile[a],len_a,window,strength);
//increase_gaps(profile[a],len_a,window,strength);
}
if (b < numseq){
/*profile[b] = make_profile(profile[b],aln->s[b],len_b,submatrix);*/
profile[b] = make_profile_new(profile[b],aln->s[b],aln->gpo[b], aln->gpe[b], aln->tgpe[b], len_b,submatrix);
}else{
weightArray_b = malloc(sizeof(float)*(len_b+2));
/*set_gap_penalties(profile[b],len_b,aln->nsip[a],strength,aln->nsip[b]);*/
set_gap_penalties_new(profile[b],len_b,aln->nsip[a],strength,aln->nsip[b], weightArray_b);
//smooth_gaps(profile[b],len_b,window,strength);
//increase_gaps(profile[b],len_b,window,strength);
}
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;
#ifdef DEBUG
fprintf(stderr,"LENA:%d LENB:%d numseq:%d\n",len_a,len_b,numseq);
#endif
if(a < numseq){
if(b < numseq){
/*map[c] = hirsch_ss_dyn(submatrix,aln->s[a],aln->s[b],hm,map[c]);[>submatrix: default=gon250mt, sequences-sequences<]*/
map[c] = hirsch_ss_dyn_new(submatrix,aln->s[a],aln->s[b],aln->gpo[a]+1,aln->gpe[a]+1, aln->tgpe[a]+1, aln->gpo[b]+1, aln->gpe[b]+1, aln->tgpe[b]+1, hm, map[c]);/*submatrix: default=gon250mt, sequences-sequences*/
}else{
hm->enda = len_b;
hm->endb = len_a;
hm->len_a = len_b;
hm->len_b = len_a;
/*map[c] = hirsch_ps_dyn(profile[b],aln->s[a],hm,map[c],aln->nsip[b]);[>profile-sequence<]*/
/*map[c] = hirsch_ps_dyn_new(profile[b],aln->s[a],aln->gpo[a]+1, aln->gpe[a]+1, aln->tgpe[a]+1, hm,map[c],aln->nsip[b]);[>profile-sequence<]*/
/*map[c] = hirsch_ps_dyn_new1(profile[b],aln->s[a],aln->gpo[a]+1, aln->gpe[a]+1, aln->tgpe[a]+1, hm,map[c],aln->nRes[b], aln->nsip[b]);[>profile-sequence<]*/
map[c] = hirsch_ps_dyn_new2(profile[b],aln->s[a],aln->gpo[a]+1, aln->gpe[a]+1, aln->tgpe[a]+1, hm,map[c],aln->nRes[b], weightArray_b, aln->nsip[b]);/*profile-sequence*/
/*map[c] = hirsch_ps_dyn_new2_test1(profile[b],aln->s[a],aln->gpo[a]+1, aln->gpe[a]+1, aln->tgpe[a]+1, hm,map[c],aln->nRes[b], weightArray_b, aln->nsip[b]);[>profile-sequence<]*/
/*map[c] = hirsch_ps_dyn_new0(profile[b],aln->s[a],aln->gpo[a]+1, aln->gpe[a]+1, aln->tgpe[a]+1, hm,map[c],aln->nsip[b]);[>profile-sequence<]*/
/*map[c] = hirsch_ps_dyn_new2_test2(profile[b],aln->s[a],aln->gpo[a]+1, aln->gpe[a]+1, aln->tgpe[a]+1, hm,map[c],aln->nRes[b], weightArray_b, aln->nsip[b]);[>profile-sequence<]*/
map[c] = mirror_hirsch_path(map[c],len_a,len_b); /*??*/
}
}else{
if(b < numseq){
/*map[c] = hirsch_ps_dyn(profile[a],aln->s[b],hm,map[c],aln->nsip[a]); [>profile-sequence<]*/
/*map[c] = hirsch_ps_dyn_new(profile[a],aln->s[b],aln->gpo[b]+1, aln->gpe[b]+1, aln->tgpe[b]+1, hm,map[c],aln->nsip[a]); [>profile-sequence<]*/
/*map[c] = hirsch_ps_dyn_new1(profile[a],aln->s[b],aln->gpo[b]+1, aln->gpe[b]+1, aln->tgpe[b]+1, hm,map[c],aln->nRes[a], aln->nsip[a]); [>profile-sequence<]*/
map[c] = hirsch_ps_dyn_new2(profile[a],aln->s[b],aln->gpo[b]+1, aln->gpe[b]+1, aln->tgpe[b]+1, hm,map[c],aln->nRes[a], weightArray_a, aln->nsip[a]); /*profile-sequence*/
/*map[c] = hirsch_ps_dyn_new0(profile[a],aln->s[b],aln->gpo[b]+1, aln->gpe[b]+1, aln->tgpe[b]+1, hm,map[c],aln->nsip[a]); [>profile-sequence<]*/
/*map[c] = hirsch_ps_dyn_new2_test1(profile[a],aln->s[b],aln->gpo[b]+1, aln->gpe[b]+1, aln->tgpe[b]+1, hm,map[c],aln->nRes[a], weightArray_a, aln->nsip[a]); [>profile-sequence<]*/
/*map[c] = hirsch_ps_dyn_new2_test2(profile[a],aln->s[b],aln->gpo[b]+1, aln->gpe[b]+1, aln->tgpe[b]+1, hm,map[c],aln->nRes[a], weightArray_a, aln->nsip[a]); [>profile-sequence<]*/
}else{
if(len_a < len_b){
/*map[c] = hirsch_pp_dyn(profile[a],profile[b],hm,map[c]); [>profile-profile<]*/
/*map[c] = hirsch_pp_dyn_new(profile[a],profile[b],hm,map[c]); [>profile-profile<]*/
/*map[c] = hirsch_pp_dyn_new0(profile[a],profile[b],aln->nRes[a],aln->nRes[b], weightArray_a, weightArray_b, hm,map[c]); [>profile-profile<]*/
map[c] = hirsch_pp_dyn_new2(profile[a],profile[b],aln->nRes[a],aln->nRes[b], weightArray_a, weightArray_b, hm,map[c]); /*profile-profile*/
/*map[c] = hirsch_pp_dyn_new2_test1(profile[a],profile[b],aln->nRes[a],aln->nRes[b], weightArray_a, weightArray_b, hm,map[c]); [>profile-profile<]*/
/*map[c] = hirsch_pp_dyn_new2_test2(profile[a],profile[b],aln->nRes[a],aln->nRes[b], aln->nsip[a], aln->nsip[b], weightArray_a, weightArray_b, hm,map[c]); [>profile-profile<]*/
}else{
hm->enda = len_b;
hm->endb = len_a;
hm->len_a = len_b;
hm->len_b = len_a;
/*map[c] = hirsch_pp_dyn(profile[b],profile[a],hm,map[c]);*/
/*map[c] = hirsch_pp_dyn_new(profile[b],profile[a],hm,map[c]);*/
/*map[c] = hirsch_pp_dyn_new0(profile[b],profile[a],aln->nRes[b], aln->nRes[a],weightArray_b, weightArray_a, hm, map[c]);*/
map[c] = hirsch_pp_dyn_new2(profile[b],profile[a],aln->nRes[b], aln->nRes[a],weightArray_b, weightArray_a, hm, map[c]);
/*map[c] = hirsch_pp_dyn_new2_test1(profile[b],profile[a],aln->nRes[b], aln->nRes[a],weightArray_b, weightArray_a, hm, map[c]);*/
/*map[c] = hirsch_pp_dyn_new2_test2(profile[b],profile[a],aln->nRes[b], aln->nRes[a],aln->nsip[b], aln->nsip[a], weightArray_b, weightArray_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);/*map[c] will be re-assigned, and the size of map[c] changed from "max(len_a,len_b) +2" to (len_a+len_b+2)*/
if(i != numseq-2){
profile[c] = malloc(sizeof(float)*64*(map[c][0]+2)); /*map[c][0] = length of consensus seq*/
/*profile[c] = update(profile[a],profile[b],profile[c],map[c],aln->nsip[a],aln->nsip[b]);*/
/*profile[c] = update_new(profile[a],profile[b],profile[c],map[c],aln->nsip[a],aln->nsip[b]);*/
profile[c] = update_new2(profile, map[c],aln, a, b, c );
#ifdef DEBUG_PROFILE1/*{{{*/
int ii = 0;
int cnt = 0;
fprintf(stderr,"\nprofile[%d](a):gpo, size = %d\n", a, len_a);
for (ii = 0; ii < map[c][0]+2; ii++ ) {
if (cnt > 0 && cnt < len_a+1){
if (!map[c][ii] || (map[c][ii] & 2)){ /*aligned or gap_B*/
fprintf(stderr,"%6.2f ", profile[a][64*cnt+55]);
cnt ++;
}else{
fprintf(stderr,"%6s ", "-");
}
}else{
fprintf(stderr,"%6.2f ", profile[a][64*cnt+55]);
cnt ++;
}
}
fprintf(stderr,"\n");
fprintf(stderr,"profile[%d](b):gpo, size = %d\n", b, len_b);
cnt = 0;
for (ii = 0; ii < map[c][0]+2; ii++ ) {
if (cnt > 0 && cnt < len_b+1){
if (!map[c][ii] || (map[c][ii] & 1)){ /*aligned or gap_A*/
fprintf(stderr,"%6.2f ", profile[b][64*cnt+55]);
cnt ++;
}else{
fprintf(stderr,"%6s ", "-");
}
}else{
fprintf(stderr,"%6.2f ", profile[b][64*cnt+55]);
cnt ++;
}
}
fprintf(stderr,"\n");
fprintf(stderr,"profile[%d](c):gpo, size = %d\n", c, map[c][0]);
for (ii = 0; ii < map[c][0]+2; ii++ ) {
fprintf(stderr,"%6.2f ", profile[c][64*ii+55]);
}
fprintf(stderr,"\n");
#endif /*}}}*/
#ifdef DEBUG_PROFILE /*{{{*/
fprintf(stderr,"\nnRes[%d](a):nRes, size = %d\n", a, len_a);
int ii = 0;
int cnt = 0;
for (ii = 1; ii < map[c][0]+1; ii++ ) {
if (!map[c][ii] || (map[c][ii] & 2)){ /*aligned or gap_B*/
fprintf(stderr,"%6d ", aln->nRes[a][cnt+1]);
cnt++;
}else{
fprintf(stderr,"%6s ", "-");
}
}
fprintf(stderr,"\n");
fprintf(stderr,"nRes[%d](b):nRes, size = %d\n", b, len_b);
cnt = 0;
for (ii = 1; ii < map[c][0]+1; ii++ ) {
if (!map[c][ii] || (map[c][ii] & 1)){ /*aligned or gap_A*/
fprintf(stderr,"%6d ", aln->nRes[b][cnt+1]);
cnt ++;
}else{
fprintf(stderr,"%6s ", "-");
}
}
fprintf(stderr,"\n");
fprintf(stderr,"nRes[%d](c):nRes, size = %d\n", c, map[c][0]);
for (ii = 1; ii < map[c][0]+1; ii++ ) {
fprintf(stderr,"%6d ", aln->nRes[c][ii]);
}
fprintf(stderr,"\n");
#endif /*}}}*/
}
aln->sl[c] = map[c][0];
aln->nsip[c] = aln->nsip[a] + aln->nsip[b]; /*nsip[c] updated here*/
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]);
if (weightArray_a){
free(weightArray_a);
}
if (weightArray_b){
free(weightArray_b);
}
}
fprintf(stderr,"\r%8.0f percent done\n",100.0);
free(profile);
hirsch_mem_free(hm);
for (i = 32;i--;){
free(submatrix[i]);
}
free(submatrix);
return map;
}/*}}}*/
int** hirschberg_alignment_against_a(struct alignment* aln,int* tree,float**submatrix, int** map,int window,float strength)/*{{{*/
{
struct hirsch_mem* hm = 0;
int i,j,g,a,b,c;
int len_a;
int len_b;
float** profile = 0;
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_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);
#ifdef DEBUG
fprintf(stderr,"\nAligning:%d %d->%d done:%f\n",a,b,c,((float)(i+1)/(float)numseq)*100);
#endif
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_mem_realloc(hm,g);
}
for (j = 0; j < (g+2);j++){
map[c][j] = -1;
}
if (a < numseq){
profile[a] = make_profile(profile[a],aln->s[a],len_a,submatrix);
}else{
set_gap_penalties(profile[a],len_a,aln->nsip[b],0,aln->nsip[a]);
//smooth_gaps(profile[a],len_a,window,strength);
//increase_gaps(profile[a],len_a,window,strength);
}
if (b < numseq){
profile[b] = make_profile(profile[b],aln->s[b],len_b,submatrix);
}else{
set_gap_penalties(profile[b],len_b,aln->nsip[a],0,aln->nsip[b]);
//smooth_gaps(profile[b],len_b,window,strength);
//increase_gaps(profile[b],len_b,window,strength);
}
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;
#ifdef DEBUG
fprintf(stderr,"LENA:%d LENB:%d numseq:%d\n",len_a,len_b,numseq);
#endif
if(a < numseq){
if(b < numseq){
map[c] = hirsch_ss_dyn(submatrix,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_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_ps_dyn(profile[a],aln->s[b],hm,map[c],aln->nsip[a]);
}else{
if(len_a < len_b){
map[c] = hirsch_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_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] = update_only_a(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_mem_free(hm);
for (i = 32;i--;){
free(submatrix[i]);
}
free(submatrix);
return map;
}/*}}}*/
/*==== sequence - sequence alignment ==== */
int* hirsch_ss_dyn(float**subm, const int* seq1,const int* seq2,struct hirsch_mem* hm, int* hirsch_path)/*{{{*/
{
int mid = ((hm->enda - hm->starta) / 2)+ hm->starta; /*the middle position of the effective alignment region for seq1, 2010-09-28 by Nanjiang*/
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;
#ifdef DEBUG
fprintf(stderr,"Forward:%d-%d %d-%d\n",hm->starta,hm->enda,hm->startb,hm->endb);
#endif
hm->f = foward_hirsch_ss_dyn(subm,seq1,seq2,hm);
hm->starta = mid;
hm->enda = old_cor[1];
#ifdef DEBUG
fprintf(stderr,"Backward:%d-%d %d-%d\n",hm->starta,hm->enda,hm->startb,hm->endb);
#endif
hm->b = backward_hirsch_ss_dyn(subm,seq1,seq2,hm);
hirsch_path = hirsch_align_two_ss_vector(subm,seq1,seq2,hm,hirsch_path,input_states,old_cor);
return 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)/*{{{*/
/*sequence to sequence alignment with position specific gap penalties*/
{
int mid = ((hm->enda - hm->starta) / 2)+ hm->starta; /*the middle position of the effective alignment region for seq1, 2010-09-28 by Nanjiang*/
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};/*store the original positions*/
if(hm->starta >= hm->enda){
return hirsch_path;
}
if(hm->startb >= hm->endb){
return hirsch_path;
}
hm->enda = mid;
if ((!gpoArray1) && (!gpeArray1) && (!tgpeArray1) && (!gpoArray2) && (!gpeArray2) && (!tgpeArray2) ){
hm->f = foward_hirsch_ss_dyn(subm,seq1,seq2,hm);
}else{
hm->f = foward_hirsch_ss_dyn_new(subm,seq1,seq2,gpoArray1,gpeArray1,tgpeArray1,gpoArray2,gpeArray2,tgpeArray2, hm);
}
#ifdef DEBUG
fprintf(stderr,"\n%s: Forward. a:%d-%d b: %d-%d\n",__FUNCTION__, hm->starta,hm->enda,hm->startb,hm->endb);
int i;
for (i = hm->startb; i <= hm->endb;i++){
fprintf(stderr,"%s: a[%d]=%f ga[%d]=%f gb[%d]=%f\n",__FUNCTION__, i, hm->f[i].a,i, hm->f[i].ga,i, hm->f[i].gb);
}
#endif
hm->starta = mid;
hm->enda = old_cor[1]; /*recover the original 'enda'*/
if ((!gpoArray1) && (!gpeArray1) && (!tgpeArray1) && (!gpoArray2) && (!gpeArray2) && (!tgpeArray2) ){
hm->b = backward_hirsch_ss_dyn(subm,seq1,seq2,hm);
}else{
hm->b = backward_hirsch_ss_dyn_new(subm,seq1,seq2,gpoArray1,gpeArray1,tgpeArray1,gpoArray2,gpeArray2,tgpeArray2, hm);
}
#ifdef DEBUG
fprintf(stderr,"\n%s: Backward. a: %d-%d b: %d-%d\n",__FUNCTION__, hm->starta,hm->enda,hm->startb,hm->endb);
for (i = hm->startb; i <= hm->endb;i++){
fprintf(stderr,"%s: a[%d]=%f ga[%d]=%f gb[%d]=%f\n",__FUNCTION__, i, hm->b[i].a,i, hm->b[i].ga,i, hm->b[i].gb);
}
#endif
if ((!gpoArray1) && (!gpeArray1) && (!tgpeArray1) && (!gpoArray2) && (!gpeArray2) && (!tgpeArray2) ){
hirsch_path = hirsch_align_two_ss_vector(subm,seq1,seq2,hm,hirsch_path,input_states,old_cor);
}else{
hirsch_path = hirsch_align_two_ss_vector_new(subm,seq1,seq2,gpoArray1,gpeArray1,tgpeArray1,gpoArray2,gpeArray2,tgpeArray2, hm,hirsch_path,input_states,old_cor);
}
return hirsch_path;
}/*}}}*/
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[])/*{{{*/
{
struct states* f = hm->f;
struct 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;
#ifdef DEBUG
fprintf(stderr,"function hirsch_align_two_ss_vector:\n");
#endif
//int max = -INFTY;
float max = -INFTY;
//float middle = (hm->endb - hm->startb)/2 + hm->startb;
float middle = (old_cor[3] - old_cor[2])/2 + old_cor[2]; /*the middle position of sequence b*/
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;
#ifdef DEBUG
fprintf(stderr,"%d-%d %f\n",hm->startb,hm->endb,sub);
#endif
if(f[i].a+b[i].a-sub > max){
max = f[i].a+b[i].a-sub;
#ifdef DEBUG
fprintf(stderr,"aligned->aligned:%f + %f = %f\n",f[i].a,b[i].a,f[i].a+b[i].a);
#endif
transition = 1;
c = i;
}
if(f[i].a+b[i].ga-gpo-sub > max){
max = f[i].a+b[i].ga-gpo-sub;
#ifdef DEBUG
fprintf(stderr,"aligned->gap_a:%f + %f +%f = %f\n",f[i].a,b[i].ga,-gpo-sub,f[i].a+b[i].ga-gpo-sub);
#endif
transition = 2;
c = i;
}
if(f[i].a+b[i].gb -gpo-sub > max){
max = f[i].a+b[i].gb - gpo-sub;
#ifdef DEBUG
fprintf(stderr,"aligned->gap_b:%f + %f +%f = %f\n",f[i].a,b[i].gb,-gpo-sub,f[i].a+b[i].gb-gpo-sub);
#endif
transition = 3;
c = i;
}
if(f[i].ga+b[i].a - gpo-sub > max){
max = f[i].ga+b[i].a - gpo-sub;
#ifdef DEBUG
fprintf(stderr,"gap_a->aligned:%f + %f + %f(gpo) = %f\n",f[i].ga,b[i].a,-gpo-sub,f[i].ga+b[i].a-gpo-sub);
#endif
transition = 5;
c = i;
}
if(hm->startb == 0){
if(f[i].gb+b[i].gb - tgpe-sub > max){
max = f[i].gb+b[i].gb -tgpe-sub;
#ifdef DEBUG
fprintf(stderr,"gap_b->gap_b:%f + %f +%f(gpe) =%f \n",f[i].gb, b[i].gb, -tgpe-sub,f[i].gb+b[i].gb-tgpe-sub);
#endif
transition = 6;
c = i;
}
}else{
if(f[i].gb+b[i].gb - gpe -sub> max){
max = f[i].gb+b[i].gb - gpe-sub;
#ifdef DEBUG
fprintf(stderr,"gap_b->gap_b:%f + %f +%f(gpe) =%f \n",f[i].gb, b[i].gb, -gpe-sub,f[i].gb+b[i].gb-gpe-sub);
#endif
transition = 6;
c = i;
}
}
if(f[i].gb+b[i].a - gpo-sub > max){
max = f[i].gb+b[i].a - gpo-sub;
#ifdef DEBUG
fprintf(stderr,"gap_b->aligned:%f + %f + %f(gpo) = %f\n",f[i].gb,b[i].a,-gpo-sub,f[i].gb+b[i].a-gpo-sub);
#endif
transition = 7;
c = i;
}
}
//i = hm->endb;
i = old_cor[3];
sub = abs(middle -i);
sub /= 1000;
if(f[i].a+b[i].gb-gpo-sub > max){
max = f[i].a+b[i].gb - gpo-sub;
#ifdef DEBUG
fprintf(stderr,"aligned->gap_b:%f + %f +%f = %f\n",f[i].a,b[i].gb,-gpo-sub,f[i].a+b[i].gb-gpo-sub);
#endif
transition = 3;
c = i;
}
if(hm->endb == hm->len_b){
if(f[i].gb+b[i].gb -tgpe-sub > max){
max = f[i].gb+b[i].gb - tgpe-sub;
#ifdef DEBUG
fprintf(stderr,"gap_b->gap_b:%f + %f +%f(gpe) =%f \n",f[i].gb, b[i].gb, -tgpe-sub,f[i].gb+b[i].gb-tgpe-sub);
#endif
transition = 6;
c = i;
}
}else{
if(f[i].gb+b[i].gb - gpe-sub > max){
max = f[i].gb+b[i].gb - gpe-sub;
#ifdef DEBUG
fprintf(stderr,"gap_b->gap_b:%f + %f +%f(gpe) =%f \n",f[i].gb, b[i].gb, -gpe-sub,f[i].gb+b[i].gb-gpe-sub);
#endif
transition = 6;
c = i;
}
}
#ifdef DEBUG
fprintf(stderr,"Transition:%d at:%d\n",transition,c);
#endif
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;
#ifdef DEBUG
/*fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);*/
/*fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);*/
fprintf(stderr,"Forward:\n");
#endif
//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 = 0.0;
hm->b[0].ga = -FLOATINFTY;
hm->b[0].gb = -FLOATINFTY;
#ifdef DEBUG
fprintf(stderr,"Using this for start:%f %f %f\n",hm->f[0].a,hm->f[0].ga,hm->f[0].gb);
#endif
hm->starta = old_cor[0];
hm->enda = old_cor[4]-1;
hm->startb = old_cor[2];
hm->endb = c-1;
#ifdef DEBUG
fprintf(stderr,"Following first: %d what:%d-%d %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
#endif
hirsch_path = hirsch_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
#ifdef DEBUG
fprintf(stderr,"Backward:\n");
#endif
//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 = 0.0;
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];
#ifdef DEBUG
fprintf(stderr,"Following last: %d what:%d-%d %d-%d\n",c+1,hm->starta,hm->enda,hm->startb,hm->endb);
#endif
hirsch_path = hirsch_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
break;
case 2:// a -> ga = 2
hirsch_path[old_cor[4]] = c;
#ifdef DEBUG
fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);
#endif
//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 = 0.0;
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;
#ifdef DEBUG
fprintf(stderr,"Following first: %d what:%d-%d %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
#endif
hirsch_path = hirsch_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 = 0.0;
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];
#ifdef DEBUG
fprintf(stderr,"Following last: %d what:%d-%d %d-%d\n",c+1,hm->starta,hm->enda,hm->startb,hm->endb);
#endif
hirsch_path = hirsch_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
break;
case 3:// a -> gb = 3
hirsch_path[old_cor[4]] = c;
#ifdef DEBUG
fprintf(stderr,"Aligning:%d-%d\n",old_cor[4],c);
#endif
//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 = 0.0;
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;
#ifdef DEBUG
fprintf(stderr,"Following first: %d what:%d-%d %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
#endif
hirsch_path = hirsch_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 = 0.0;
hm->b[0].a = input_states[3];
hm->b[0].ga = input_states[4];
hm->b[0].gb = input_states[5];
#ifdef DEBUG
fprintf(stderr,"Following last: %d\n",c+1);
#endif
hirsch_path = hirsch_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
break;
case 5://ga -> a = 5
hirsch_path[old_cor[4]+1] = c+1;
#ifdef DEBUG
fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);
#endif
//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 = 0.0;
hm->b[0].gb = -FLOATINFTY;
hm->starta = old_cor[0];
hm->enda = old_cor[4];
hm->startb = old_cor[2];
hm->endb = c-1;
#ifdef DEBUG
fprintf(stderr,"Following first: %d what:%d-%d %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
#endif
hirsch_path = hirsch_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 = 0.0;
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];
#ifdef DEBUG
fprintf(stderr,"Following last: %d\n",c+1);
#endif
hirsch_path = hirsch_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 = 0.0;
hm->starta = old_cor[0];
hm->enda = old_cor[4]-1;
hm->startb = old_cor[2];
hm->endb = c;
#ifdef DEBUG
fprintf(stderr,"Following first: %d what:%d-%d %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
#endif
hirsch_path = hirsch_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 = 0.0;
hm->b[0].a = input_states[3];
hm->b[0].ga = input_states[4];
hm->b[0].gb = input_states[5];
#ifdef DEBUG
fprintf(stderr,"Following last: %d\n",c+1);
#endif
hirsch_path = hirsch_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
break;
case 7://gb->a = 7;
hirsch_path[old_cor[4]+1] = c+1;
#ifdef DEBUG
fprintf(stderr,"Aligning:%d-%d\n",old_cor[4]+1,c+1);
#endif
//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 = 0.0;
hm->starta = old_cor[0];
hm->enda = old_cor[4]-1;
hm->startb = old_cor[2];
hm->endb = c;
#ifdef DEBUG
fprintf(stderr,"Following first: %d what:%d-%d %d-%d\n",c-1,hm->starta,hm->enda,hm->startb,hm->endb);
#endif
hirsch_path = hirsch_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 = 0.0;
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];
#ifdef DEBUG
fprintf(stderr,"Following last: %d\n",c+1);
#endif
hirsch_path = hirsch_ss_dyn(subm,seq1,seq2,hm,hirsch_path);
break;
}
return hirsch_path;
}/*}}}*/
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[] )/*{{{*/
{
struct states* f = hm->f;
struct states* b = hm->b;
int i,j,c;
int transition = -1;
//transition code:
// a -> a = 1
// a -> ga = 2
// a -> gb = 3
// ga-> ga = 4
// ga-> a = 5
// gb-> gb = 6;
// gb-> a = 7;
int mid_a = old_cor[4];
mid_a ++;
#ifdef DEBUG
fprintf(stderr,"\nFunction:%s\n", __FUNCTION__);
#endif
//int max = -INFTY;
float max = -INFTY;
//float middle = (hm->endb - hm->startb)/2 + hm->startb;
float middle = (old_cor[3] - old_cor[2])/2 + old_cor[2]; /*the middle position of sequence b*/
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); /*position related value ?? what is it for*/
sub /= 1000;
#ifdef DEBUG
fprintf(stderr,"startb:endb %d-%d sub=%f\n",hm->startb,hm->endb,sub);
#endif
if(f[i].a+b[i].a-sub > max){
max = f[i].a+b[i].a-sub;
#ifdef DEBUG
fprintf(stderr,"i=%d\t aligned->aligned:%f + %f = %f\n",i,f[i].a,b[i].a,f[i].a+b[i].a);
#endif
transition = 1;
c = i;
}
/*if(f[i].a+b[i].ga-gpo-sub > max){*/
if(f[i].a+b[i].ga-gpoArray1[mid_a]-sub > max){
max = f[i].a+b[i].ga-gpoArray1[mid_a]-sub;
#ifdef DEBUG
fprintf(stderr,"i=%d\t aligned->gap_a:%f + %f +%f = %f\n",i,f[i].a,b[i].ga,-gpoArray1[mid_a]-sub,f[i].a+b[i].ga-gpoArray1[mid_a]-sub);
#endif
transition = 2;
c = i;
}
/*if(f[i].a+b[i].gb -gpo-sub > max){*/
if(f[i].a+b[i].gb -gpoArray2[i]-sub > max){
max = f[i].a+b[i].gb - gpoArray2[i]-sub;
#ifdef DEBUG
fprintf(stderr,"i=%d\t aligned->gap_b:%f + %f +%f = %f\n",i,f[i].a,b[i].gb,-gpoArray2[i]-sub,f[i].a+b[i].gb-gpoArray2[i]-sub);
#endif
transition = 3;
c = i;
}
/*if(f[i].ga+b[i].a - gpo-sub > max){*/
if(f[i].ga+b[i].a - gpoArray1[mid_a-1]-sub > max){
max = f[i].ga+b[i].a - gpoArray1[mid_a-1]-sub;
#ifdef DEBUG
fprintf(stderr,"i=%d\t gap_a->aligned:%f + %f + %f(gpo) = %f\n",i, f[i].ga,b[i].a,-gpoArray1[mid_a-1]-sub,f[i].ga+b[i].a-gpoArray1[mid_a-1]-sub);
#endif
transition = 5;
c = i;
}