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kalignP_dp.c
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/*
kalignP_dp.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"
int* f_only_pp_dyn(int* path, struct dp_matrix *dp,const float* fprof1,const float* fprof2,const int len_a,const int len_b,int fdim,int stride)
{
// unsigned int freq[26];
struct states* s = 0;
char** trace = 0;
char* tracep = 0;
register float pa = 0;
register float pga = 0;
register float pgb = 0;
register float ca = 0;
register int i = 0;
register int j = 0;
register int c = 0;
register int f = 0;
s = dp->s;
trace = dp->tb;
trace[len_a][len_b] = 32;
fprof1 += len_a * stride;
s[len_b].a = 0.0;
s[len_b].ga = -FLOATINFTY;
s[len_b].gb = -FLOATINFTY;
//init of first row;
tracep = trace[len_a];
j = len_b;
while(--j){
s[j].a = -FLOATINFTY;
//s[j].ga = 0;
s[j].ga = s[j+1].a;//+prof2[29];
if (s[j+1].ga > s[j].ga){
s[j].ga = s[j+1].ga ;
}
s[j].gb = -FLOATINFTY;
tracep[j] = 8;
}
s[0].a = -FLOATINFTY;
s[0].ga = -FLOATINFTY;
s[0].gb = -FLOATINFTY;
i = len_a;
while(--i){
fprof1 -= stride;
tracep = trace[i];
pa = s[len_b].a;
pga = s[len_b].ga;
pgb = s[len_b].gb;
s[len_b].a = -FLOATINFTY;
s[len_b].ga = -FLOATINFTY;
//s[len_b].gb = 0;
s[len_b].gb = pa;//+prof1[29];
if(pgb > s[len_b].gb){
s[len_b].gb = pgb;
}
tracep[len_b] = 16;
j = len_b;
fprof2 += len_b * stride;
while(--j){
fprof2 -= stride;
ca = s[j].a;
c = 1;
if((pga) > pa){
pa = pga;
c = 2;
}
if((pgb) > pa){
pa = pgb;
c = 4;
}
for (f = 0; f < fdim;f++){
// fprintf(stderr,"%d %d: %d\n",i,j,fprof1[pga] * fprof2[pga+fdim]);
pa += fprof1[f] * fprof2[f+fdim];
}
s[j].a = pa;
pga = s[j].ga;
s[j].ga = s[j+1].a;
if (s[j+1].ga > s[j].ga){
s[j].ga = s[j+1].ga;
c |= 8;
}
pgb = s[j].gb;
s[j].gb = ca;
if(pgb > s[j].gb){
s[j].gb = pgb;
c |= 16;
}
tracep[j] = c;
pa = ca;
}
fprof2 -= stride;
//LAST CELL (0)
ca = s[0].a;
c = 1;
if((pga) > pa){
pa = pga;
c = 2;
}
if((pgb) > pa){
pa = pgb;
c = 4;
}
for (f = 0; f < fdim;f++){
// fprintf(stderr,"%d %d: %d\n",i,j,fprof1[pga] * fprof2[pga+fdim]);
pa += fprof1[f] * fprof2[f+fdim];
}
s[0].a = pa;
s[0].ga = -FLOATINFTY;
pgb = s[0].gb;
s[0].gb = ca;
if(pgb> s[0].gb){
s[0].gb = pgb;
c |= 16;
}
tracep[0] = c;
}
fprof1 -= stride;
tracep = trace[0];
j = len_b;
fprof2 += len_b * stride;
pa = s[j].a;
pga = s[j].ga;
pgb = s[j].gb;
s[j].a = -FLOATINFTY;
s[j].ga = -FLOATINFTY;
//s[j].gb = -INFTY;
s[len_b].gb = pa;//+prof1[29];
if(pgb > s[len_b].gb){
s[len_b].gb = pgb;
}
while(--j){
fprof2 -= stride;
ca = s[j].a;
c = 1;
if((pga) > pa){
pa = pga;
c = 2;
}
if((pgb) > pa){
pa = pgb;
c = 4;
}
for (f = 0; f < fdim;f++){
pa += fprof1[f] * fprof2[f+fdim];
// fprintf(stderr,"%d %d: %d\n",i,j,fprof1[pga] * fprof2[pga+fdim]);
}
s[j].a = pa;
pga = s[j].ga;
s[j].ga = s[j+1].a;
if (s[j+1].ga > s[j].ga){
s[j].ga = s[j+1].ga;
c |= 8;
}
pgb = s[j].gb;
s[j].gb = -FLOATINFTY;
tracep[j] = c;
pa = ca;
}
fprof2 -= stride;
ca = s[0].a;
c = 1;
if((pga) > pa){
pa = pga;
c = 2;
}
if((pgb) > pa){
pa = pgb;
c = 4;
}
for (f = 0; f < fdim;f++){
pa += fprof1[f] * fprof2[f+fdim];
// fprintf(stderr,"%d %d: %d\n",i,j,fprof1[pga] * fprof2[pga+fdim]);
}
s[0].a = pa;
s[0].ga = s[1].a;
if (s[1].ga > s[0].ga){
s[0].ga = s[1].ga;
c |= 8;
}
pgb = s[0].gb;
s[0].gb = ca;
if(pgb> s[0].gb){
s[0].gb = pgb;
c |= 16;
}
tracep[0] = c;
pgb = s[0].gb;
c = 2;
if(s[0].ga > pgb){
pgb = s[0].ga;
c = 1;
}
if(s[0].a >= pgb){
pgb = s[0].a;
c = 0;
}
//fprintf(stderr,"SCORE:%d\n",ca);
ca = c;
i = 0;
j = 0;
f = 1;
while(trace[i][j] < 32){
// fprintf(stderr,"%d->%d %d:%d %d:%d\n",c,trace[i][j],i,j,len_a,len_b);
switch(f){
case 0:
if (trace[i][j] & 2){
f = 1;
if(i+1!= len_a){
path[c+1] |= 16;
// fprintf(stderr,"GAP_CLOSE\n");
}else{
path[c+1] |= 32+16;
}
}else if (trace[i][j] & 4){
f = 2;
if(j+1!= len_b){
path[c+1] |= 16;
// fprintf(stderr,"GAP_CLOSE\n");
}else{
path[c+1] |= 32+16;
}
}
//path[c] = 0;
i++;
j++;
break;
case 1:
if(trace[i][j] & 8){
f = 1;
if(i!=0 && i!= len_a){
// / fprintf(stderr,"GAP_EXT\n");
if(!(path[c]&16)){
path[c] |= 8;
}
}else{
if(!(path[c]&16)){
path[c] |= 32+8;
}
}
}else{
f = 0;
if(i!=0 && i!= len_a){
// fprintf(stderr,"GAP_OPEN\n");
path[c] |= 4;
}else{
path[c] |= 32+4;
}
}
path[c] |= 1;
j++;
break;
case 2:
if(trace[i][j] & 16){
f = 2;
if(j !=0 && j != len_b){
// fprintf(stderr,"GAP_EXT\n");
if(!(path[c]&16)){
path[c] |= 8;
}
}else{
if(!(path[c]&16)){
path[c] |= 32+8;
}
}
}else{
f = 0;
if(j!=0 && j != len_b){
// fprintf(stderr,"GAP_OPEN\n");
path[c] |= 4;
}else{
path[c] |= 32+4;
}
}
path[c] |= 2;
i++;
break;
}
c++;
}
path[0] = c-1;
path[c] = 3;
path[c+1] = pgb;
return path;
}
int* fpp_dyn(int* path, struct dp_matrix *dp,const float* prof1,const float* prof2,const float* fprof1,const float* fprof2,const int len_a,const int len_b,int fdim,int stride)
{
unsigned int freq[26];
struct states* s = 0;
char** trace = 0;
char* tracep = 0;
register float pa = 0;
register float pga = 0;
register float pgb = 0;
register float ca = 0;
register int i = 0;
register int j = 0;
register int c = 0;
register int f = 0;
s = dp->s;
trace = dp->tb;
trace[len_a][len_b] = 32;
prof1 += len_a << 6;
fprof1 += len_a * stride;
s[len_b].a = 0;
s[len_b].ga = -FLOATINFTY;
s[len_b].gb = -FLOATINFTY;
//init of first row;
tracep = trace[len_a];
j = len_b;
while(--j){
s[j].a = -FLOATINFTY;
//s[j].ga = 0;
s[j].ga = s[j+1].a+prof2[29];//+prof2[29];
if (s[j+1].ga+prof2[29] > s[j].ga){
s[j].ga = s[j+1].ga+prof2[29];
}
s[j].gb = -FLOATINFTY;
tracep[j] = 8;
}
s[0].a = -FLOATINFTY;
s[0].ga = -FLOATINFTY;
s[0].gb = -FLOATINFTY;
i = len_a;
while(--i){
prof1 -= 64;
fprof1 -= stride;
c = 1;
for (j = 26; j--;){
if(prof1[j]){
freq[c] = j;
c++;
}
}
freq[0] = c;
tracep = trace[i];
pa = s[len_b].a;
pga = s[len_b].ga;
pgb = s[len_b].gb;
s[len_b].a = -FLOATINFTY;
s[len_b].ga = -FLOATINFTY;
//s[len_b].gb = 0;
s[len_b].gb = pa+prof1[29];//+prof1[29];
if(pgb+prof1[29] > s[len_b].gb){
s[len_b].gb = pgb+prof1[29];
}
tracep[len_b] = 16;
j = len_b;
prof2 += len_b << 6;
fprof2 += len_b * stride;
while(--j){
prof2 -= 64;
fprof2 -= stride;
ca = s[j].a;
c = 1;
if((pga += prof2[91]) > pa){
pa = pga;
c = 2;
}
if((pgb += prof1[91]) > pa){
pa = pgb;
c = 4;
}
prof2 += 32;
for (f = freq[0];--f;){
pa += prof1[freq[f]]*prof2[freq[f]];
}
prof2 -= 32;
for (f = 0; f < fdim;f++){
// fprintf(stderr,"%d %d: %d\n",i,j,fprof1[pga] * fprof2[pga+fdim]);
pa += fprof1[f] * fprof2[f+fdim];
}
s[j].a = pa;
pga = s[j].ga;
s[j].ga = s[j+1].a+prof2[27];
if (s[j+1].ga+prof2[28] > s[j].ga){
s[j].ga = s[j+1].ga+prof2[28];
c |= 8;
}
pgb = s[j].gb;
s[j].gb = ca+prof1[27];
if(pgb+prof1[28] > s[j].gb){
s[j].gb = pgb+prof1[28];
c |= 16;
}
tracep[j] = c;
pa = ca;
}
prof2 -= 64;
fprof2 -= stride;
//LAST CELL (0)
ca = s[0].a;
c = 1;
if((pga+=prof2[91]) > pa){
pa = pga;
c = 2;
}
if((pgb+=prof1[91]) > pa){
pa = pgb;
c = 4;
}
prof2 += 32;
for (f = freq[0];--f;){
pa += prof1[freq[f]]*prof2[freq[f]];
}
prof2 -= 32;
for (f = 0; f < fdim;f++){
// fprintf(stderr,"%d %d: %d\n",i,j,fprof1[pga] * fprof2[pga+fdim]);
pa += fprof1[f] * fprof2[f+fdim];
}
s[0].a = pa;
s[0].ga = -FLOATINFTY;
pgb = s[0].gb;
s[0].gb = ca+prof1[27]+prof1[29];
if(pgb+prof1[29] > s[0].gb){
s[0].gb = pgb+prof1[29];
c |= 16;
}
tracep[0] = c;
}
prof1 -= 64;
fprof1 -= stride;
c = 1;
for (j = 26; j--;){
if(prof1[j]){
freq[c] = j;
c++;
}
}
freq[0] = c;
tracep = trace[0];
j = len_b;
prof2 += len_b << 6;
fprof2 += len_b * stride;
pa = s[j].a;
pga = s[j].ga;
pgb = s[j].gb;
s[j].a = -FLOATINFTY;
s[j].ga = -FLOATINFTY;
//s[j].gb = -INFTY;
s[len_b].gb = pa+prof1[29];//+prof1[29];
if(pgb+prof1[29] > s[len_b].gb){
s[len_b].gb = pgb+prof1[29];
}
while(--j){
prof2 -= 64;
fprof2 -= stride;
ca = s[j].a;
c = 1;
if((pga+=prof2[91]) > pa){
pa = pga;
c = 2;
}
if((pgb+=prof1[91]) > pa){
pa = pgb;
c = 4;
}
prof2+=32;
for (f = freq[0];--f;){
pa += prof1[freq[f]]*prof2[freq[f]];
}
prof2-=32;
for (f = 0; f < fdim;f++){
pa += fprof1[f] * fprof2[f+fdim];
// fprintf(stderr,"%d %d: %d\n",i,j,fprof1[pga] * fprof2[pga+fdim]);
}
s[j].a = pa;
pga = s[j].ga;
s[j].ga = s[j+1].a+prof2[27]+prof2[29];
if (s[j+1].ga+prof2[29] > s[j].ga){
s[j].ga = s[j+1].ga+prof2[29];
c |= 8;
}
pgb = s[j].gb;
s[j].gb = -FLOATINFTY;
tracep[j] = c;
pa = ca;
}
prof2 -= 64;
fprof2 -= stride;
ca = s[0].a;
c = 1;
if((pga+=prof2[91]) > pa){
pa = pga;
c = 2;
}
if((pgb+=prof1[91]) > pa){
pa = pgb;
c = 4;
}
prof2+=32;
for (f = freq[0];--f;){
pa += prof1[freq[f]]*prof2[freq[f]];
}
prof2-=32;
for (f = 0; f < fdim;f++){
pa += fprof1[f] * fprof2[f+fdim];
// fprintf(stderr,"%d %d: %d\n",i,j,fprof1[pga] * fprof2[pga+fdim]);
}
s[0].a = pa;
s[0].ga = s[1].a+prof2[27]+prof2[29];
if (s[1].ga+prof2[29] > s[0].ga){
s[0].ga = s[1].ga+prof2[29];
c |= 8;
}
pgb = s[0].gb;
s[0].gb = ca+prof1[27]+prof1[29];
if(pgb +prof1[29]> s[0].gb){
s[0].gb = pgb+prof1[29];
c |= 16;
}
tracep[0] = c;
pgb = s[0].gb;
c = 2;
if(s[0].ga > pgb){
pgb = s[0].ga;
c = 1;
}
if(s[0].a >= pgb){
pgb = s[0].a;
c = 0;
}
//fprintf(stderr,"SCORE:%d\n",ca);
f = c;
i = 0;
j = 0;
c = 1;
while(trace[i][j] < 32){
// fprintf(stderr,"%d->%d %d:%d %d:%d\n",c,trace[i][j],i,j,len_a,len_b);
switch(f){
case 0:
if (trace[i][j] & 2){
f = 1;
if(i+1!= len_a){
path[c+1] |= 16;
// fprintf(stderr,"GAP_CLOSE\n");
}else{
path[c+1] |= 32+16;
}
}else if (trace[i][j] & 4){
f = 2;
if(j+1!= len_b){
path[c+1] |= 16;
// fprintf(stderr,"GAP_CLOSE\n");
}else{
path[c+1] |= 32+16;
}
}
//path[c] = 0;
i++;
j++;
break;
case 1:
if(trace[i][j] & 8){
f = 1;
if(i!=0 && i!= len_a){
// / fprintf(stderr,"GAP_EXT\n");
if(!(path[c]&16)){
path[c] |= 8;
}
}else{
if(!(path[c]&16)){
path[c] |= 32+8;
}
}
}else{
f = 0;
if(i!=0 && i!= len_a){
// fprintf(stderr,"GAP_OPEN\n");
path[c] |= 4;
}else{
path[c] |= 32+4;
}
}
path[c] |= 1;
j++;
break;
case 2:
if(trace[i][j] & 16){
f = 2;
if(j !=0 && j != len_b){
// fprintf(stderr,"GAP_EXT\n");
if(!(path[c]&16)){
path[c] |= 8;
}
}else{
if(!(path[c]&16)){
path[c] |= 32+8;
}
}
}else{
f = 0;
if(j!=0 && j != len_b){
// fprintf(stderr,"GAP_OPEN\n");
path[c] |= 4;
}else{
path[c] |= 32+4;
}
}
path[c] |= 2;
i++;
break;
}
c++;
}
path[0] = c-1;
path[c] = 3;
path[c+1] = pgb;
return path;
}
/*
int* dna_pp_dyn(int* path, struct dp_matrix *dp,const int* prof1,const int* prof2,const int len_a,const int len_b)
{
struct states* s = 0;
char** trace = 0;
char* tracep = 0;
register int pa = 0;
register int pga = 0;
register int pgb = 0;
register int ca = 0;
register int i = 0;
register int j = 0;
register int c = 0;
s = dp->s;
trace = dp->tb;
trace[len_a][len_b] = 32;
prof1 += len_a * 22;
s[len_b].a = 0;
s[len_b].ga = -INFTY;
s[len_b].gb = -INFTY;
//init of first row;
tracep = trace[len_a];
j = len_b;
while(--j){
s[j].a = -INFTY;
//s[j].ga = 0;
s[j].ga = s[j+1].a+prof2[10];//+prof2[29];
if (s[j+1].ga+prof2[10] > s[j].ga){
s[j].ga = s[j+1].ga+prof2[10];
}
s[j].gb = -INFTY;
tracep[j] = 8;
}
s[0].a = -INFTY;
s[0].ga = -INFTY;
s[0].gb = -INFTY;
i = len_a;
while(--i){
prof1 -= 22;
tracep = trace[i];
pa = s[len_b].a;
pga = s[len_b].ga;
pgb = s[len_b].gb;
s[len_b].a = -INFTY;
s[len_b].ga = -INFTY;
//s[len_b].gb = 0;
s[len_b].gb = pa+prof1[10];//+prof1[29];
if(pgb+prof1[10] > s[len_b].gb){
s[len_b].gb = pgb+prof1[10];
}
tracep[len_b] = 16;
j = len_b;
prof2 += len_b *22;
while(--j){
prof2 -= 22;
ca = s[j].a;
c = 1;
if((pga += prof2[30]) > pa){
pa = pga;
c = 2;
}
if((pgb += prof1[30]) > pa){
pa = pgb;
c = 4;
}
prof2 += 11;
for (pga = 8;pga--;){
pa += prof1[pga]*prof2[pga];
}
prof2 -= 11;
s[j].a = pa;
pga = s[j].ga;
s[j].ga = s[j+1].a+prof2[8];
if (s[j+1].ga+prof2[9] > s[j].ga){
s[j].ga = s[j+1].ga+prof2[9];
c |= 8;
}
pgb = s[j].gb;
s[j].gb = ca+prof1[8];
if(pgb+prof1[9] > s[j].gb){
s[j].gb = pgb+prof1[9];
c |= 16;
}
tracep[j] = c;
pa = ca;
}
prof2 -= 22;
//LAST CELL (0)
ca = s[0].a;
c = 1;
if((pga+=prof2[30]) > pa){
pa = pga;
c = 2;
}
if((pgb+=prof1[30]) > pa){
pa = pgb;
c = 4;
}
prof2 += 11;
for (pga = 8;pga--;){
pa += prof1[pga]*prof2[pga];
}
prof2 -= 11;
s[0].a = pa;
s[0].ga = -INFTY;
pgb = s[0].gb;
s[0].gb = ca+prof1[8]+prof1[10];
if(pgb+prof1[10] > s[0].gb){
s[0].gb = pgb+prof1[10];
c |= 16;
}
tracep[0] = c;
}
prof1 -= 22;
tracep = trace[0];
j = len_b;
prof2 += len_b *22;
pa = s[j].a;
pga = s[j].ga;
pgb = s[j].gb;
s[j].a = -INFTY;
s[j].ga = -INFTY;
//s[j].gb = -INFTY;
s[len_b].gb = pa+prof1[10];//+prof1[29];
if(pgb+prof1[10] > s[len_b].gb){
s[len_b].gb = pgb+prof1[10];
}
while(--j){
prof2 -= 22;
ca = s[j].a;
c = 1;
if((pga+=prof2[30]) > pa){
pa = pga;
c = 2;
}
if((pgb+=prof1[30]) > pa){
pa = pgb;
c = 4;
}
prof2+=11;
for (pga = 8;pga--;){
pa += prof1[pga]*prof2[pga];
}
prof2-=11;
s[j].a = pa;
pga = s[j].ga;
s[j].ga = s[j+1].a+prof2[2]+prof2[10];
if (s[j+1].ga+prof2[10] > s[j].ga){
s[j].ga = s[j+1].ga+prof2[10];
c |= 8;
}
pgb = s[j].gb;
s[j].gb = -INFTY;
tracep[j] = c;
pa = ca;
}
prof2 -= 22;
ca = s[0].a;
c = 1;
if((pga+=prof2[30]) > pa){
pa = pga;
c = 2;
}
if((pgb+=prof1[30]) > pa){
pa = pgb;
c = 4;
}
prof2+=11;
for (pga = 8;pga--;){
pa += prof1[pga]*prof2[pga];
}
prof2-=11;
s[0].a = pa;
s[0].ga = s[1].a+prof2[8]+prof2[10];
if (s[1].ga+prof2[10] > s[0].ga){
s[0].ga = s[1].ga+prof2[10];
c |= 8;
}
pgb = s[0].gb;
s[0].gb = ca+prof1[8]+prof1[10];