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myFold_MFT-nz.c
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myFold_MFT-nz.c
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#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <ctype.h>
// TODO: these files appear to be identical.
#ifdef DNA
#include "myFold_newpen_DNA.h"
#else
#include "myFold_newpen.h"
#endif
#ifdef DNA
#define BINPREFIX "dnabin/"
#else
#define BINPREFIX ""
#endif
#define NEW_RULES 1
#ifndef NEW_RULES
#error "Choice of terminal mismatch rules unspecified (#define NEW_RULES in myFold_MFT.c)"
#endif
extern int nucenergy[6];
extern int g0;
int affinePent (int a, int b );
int retnucenergy ( int a );
int valid_pair(int i,int j);
void setup(void) {
int i,j;
/*
Allocate memory for the matrices
*/
for( i = 0; i < NUM_MATRICES; i++ ){
the_matrices[i] = (int**) malloc( (len_s+5+DUMMY_LENGTH*2)*sizeof(int*) );
if(the_matrices[i] == NULL){
printf("Error allocating memory for matrix %d\n",i);
exit(1);
}
for( j = 0; j <= len_s+DUMMY_LENGTH*2; j++ ){
the_matrices[i][j] = (int *) malloc( (len_t+5+DUMMY_LENGTH*2)*sizeof(int) );
if(the_matrices[i][j] == NULL){
printf("Error allocating memory for matrix %d, row %d\n",i,j);
exit(1);
}
}
}
/*
Allocate memory for the asymmetric loop matrices
*/
lu = (struct asymloopdata**) malloc( (len_s+1+DUMMY_LENGTH*2)*sizeof(struct asymloopdata*) );
ld = (struct asymloopdata**) malloc( (len_s+1+DUMMY_LENGTH*2)*sizeof(struct asymloopdata*) );
l1xn = (struct asymloopdata**) malloc( (len_s+1+DUMMY_LENGTH*2)*sizeof(struct asymloopdata*) );
lnx1 = (struct asymloopdata**) malloc( (len_s+1+DUMMY_LENGTH*2)*sizeof(struct asymloopdata*) );
for( i = 0; i <= len_s + DUMMY_LENGTH*2; i++){
lu[i] = (struct asymloopdata*) malloc( (len_t + 1 + DUMMY_LENGTH*2)*sizeof(struct asymloopdata) );
ld[i] = (struct asymloopdata*) malloc( (len_t + 1 + DUMMY_LENGTH*2)*sizeof(struct asymloopdata) );
l1xn[i] = (struct asymloopdata*) malloc( (len_t + 1 + DUMMY_LENGTH*2)*sizeof(struct asymloopdata) );
lnx1[i] = (struct asymloopdata*) malloc( (len_t + 1 + DUMMY_LENGTH*2)*sizeof(struct asymloopdata) );
}
//assign aliases for quick typing
pxp = the_matrices[PXP_M];
bu = the_matrices[BU_M];
bd = the_matrices[BD_M];
bu2 = the_matrices[BU2_M];
bd2 = the_matrices[BD2_M];
f = the_matrices[F_M];
//get the nearest neighbor energies from the files
get_stack_energies();
get_iloop_energies();
//allocate memory for the pairing matrix
pairs = (int **)malloc( (len_s+DUMMY_LENGTH)*sizeof(int*) );
if(pairs == NULL){
printf( "Failed to allocate memory for pairs\n");
exit(1);
}
for( i = 0; i < len_s + DUMMY_LENGTH; i++ ){
pairs[i] = (int *)malloc( (len_t+DUMMY_LENGTH)*sizeof(int) );
if(pairs[i] == NULL){
printf( "Failed to allocate memory for pairs[%d]\n", i);
exit(1);
}
}
//allocate some initial memory for the structure list
structures = (struct loop*) malloc( 10*sizeof(struct loop) );
}
/*
takes a character string and encodes it into the numerical array
used in the algorithm. direction is a flag which tells whether the output is
5' to 3' or 3' to 5'. If direction is 1, the output is 5' to 3'. Otherwise it is 3' to 5'.
The s should be 5' to 3' and the t should be 3' to 5'.
*/
void encode(int* dest, const char* src, const int length, const int direction){
int i;
//add the buffers at the beginning and end
for( i = 0; i < DUMMY_LENGTH; i++ ){
dest[i] = X; //pad the beginning with 'X's
dest[i+length+DUMMY_LENGTH] = X; //pad the end with 'X's
}
//encode the sequences
// A=0, C=1, G=2, U=3, X=4, *=5 ( X is non-pairing misc. base and * indicates a gap)
if(direction == 1){ // the s sequence
for( i = 0; i < length; i++){
char c = toupper( src[i] ); //convert all characters to upper case
switch(c){
case 'A':
dest[i+DUMMY_LENGTH] = A;
break;
case 'C':
dest[i+DUMMY_LENGTH] = C;
break;
case 'G':
dest[i+DUMMY_LENGTH] = G;
break;
case 'U':
dest[i+DUMMY_LENGTH] = U;
break;
case 'T':
dest[i+DUMMY_LENGTH] = U; // rna vs. dna
break;
default:
dest[i+DUMMY_LENGTH] = X; //if not a,c,g or u, make it an 'X'
}
}
}
else{ // or the t sequence
for( i = 0; i < length; i++){ // t is entered 5' to 3'. Flip it to 3' to 5'
char c = toupper( src[length - i -1] );
switch(c){
case 'A':
dest[i+DUMMY_LENGTH] = A;
break;
case 'C':
dest[i+DUMMY_LENGTH] = C;
break;
case 'G':
dest[i+DUMMY_LENGTH] = G;
break;
case 'U':
dest[i+DUMMY_LENGTH] = U;
break;
case 'T':
dest[i+DUMMY_LENGTH] = U; // rna vs. dna
break;
default:
dest[i+DUMMY_LENGTH] = X; //if not a,c,g or u, make it an 'X'
}
}
}
}
/*
------------------------ fill_arrays ----------------------
proceeds through the process of filling the matrices
*/
void fill_arrays(void){
int i,j,k;
/*int penalize = 0; //removed 31 Oct 2011 JH: for oligo-oligo binding, use non-MFT version
if(len_t > PENALTY_THRESHOLD)
penalize = 1;*/
/*************************
** INITIALIZIATION **
*************************/
//initialize all matrices to negative infinity (-9999)
for( i = 0; i < NUM_MATRICES; i++ ){
for( j = 0; j <= len_s+DUMMY_LENGTH*2; j++ ){
for( k = 0; k <= len_t+DUMMY_LENGTH*2; k++ ){
the_matrices[i][j][k] = NEG_INFINITY;
}
}
}
for( i = 0; i <= len_s+DUMMY_LENGTH*2; i++){
for( j = 0; j <= len_t+DUMMY_LENGTH*2; j++ ){
lu[i][j].score = -23423; //NEG_INFINITY*3;
ld[i][j].score = -28923; //NEG_INFINITY*3;
l1xn[i][j].score = -29387; //NEG_INFINITY*3;
lnx1[i][j].score = -9823; //NEG_INFINITY*3;
lu[i][j].up = lu[i][j].down = ld[i][j].up = ld[i][j].down = 99;
l1xn[i][j].up = l1xn[i][j].down = lnx1[i][j].up = lnx1[i][j].down = 99;
}
}
//reallocate memory to structures to make it an appropriate size
structures = (struct loop*) realloc(structures, (len_s+len_t+DUMMY_LENGTH*2)*sizeof(struct loop));
numstructures = 0;
/***********************
** ALGORITHM **
***********************/
/*
Equivalents to the paper (diagram and supplementary material):
au_penalty is the \delta G_{AU/GU} term
pxp : M matrix
bu : B
bu2 : B2
bd : b
bd2 : b2
lu : A
ld : a
*/
//consider the initial conditions
//when you are computing matrix entries too small for proper bulge loop calculations
for( i = DUMMY_LENGTH; i <= len_s+DUMMY_LENGTH+1; i++ ){
for( j = DUMMY_LENGTH; j <= len_t+DUMMY_LENGTH+1; j++ ){
//printf("(%d,%d) :: %c %c // %d\n",i,j,num_to_base(s[i]),num_to_base(t[j]),match(i+1,j+1));
int t1, t2, t3, t4, t5, t6; // temporary variables 1-6
//make sure that matrix only gets filled at valid pairings.
//if(valid_pair(i,j)) {
t1 = pxp[i-1][j-1] + match(i,j) + affinePent(j,j); // i, j pair #aa
t2 = pxp[i-2][j-2] + i11(i,j) + affinePent(j-1,j); // 1x1 internal loop #bb
t3 = pxp[i-2][j-3] + i12(i,j) + affinePent(j-2,j); // 1x2 internal loop #cc
t4 = pxp[i-3][j-2] + i21(i,j) + affinePent(j-1,j); // 2x1 internal loop #dd
t5 = pxp[i-3][j-3] + i22(i,j) + affinePent(j-2,j); // 2x2 internal loop #ee
t6 = pxp[i-2][j-1] + matchAlt(i-2,i,j-1,j) - SINGLE_GAP_PENALTY + retnucenergy(j); // bulge loop in s #ff
pxp[i][j] = MAX(t1, MAX(t2, MAX(t3, MAX(t4, MAX(t5, t6)))));
t1 = pxp[i-1][j-2] + matchAlt(i-1,i,j-2,j) - SINGLE_GAP_PENALTY + affinePent(j-1,j); // bulge loop in t #gg
//t6 = startmatch(i,j) - INITIATION_PENALTY - g0 + retnucenergy(j); // first pair #ww
t6 = startmatch(i,j) - INITIATION_PENALTY - g0 + affinePent(j,j); // first pair #ww
pxp[i][j] = MAX(pxp[i][j], MAX(t1, t6));
////make sure that matrix only gets filled at valid pairings.
if(valid_pair(i-1,j-1)) {
t2 = bu[i-1][j-1] + au_penalty(i,j) + retnucenergy(j); // closing bulge loop in s, i and j binding #hh
t3 = bd[i-1][j-1] + au_penalty(i,j) + retnucenergy(j); // bulge loop in t closing, i and j binding #ii
t4 = lu[i-1][j-1].score + tmatch2(i,j) + retnucenergy(j); // terminal match after asym internal loop #jj
t5 = ld[i-1][j-1].score + tmatch2(i,j) + retnucenergy(j); // terminal match after asym internal loop #kk
pxp[i][j] = MAX(pxp[i][j], MAX(t2, MAX(t3, MAX(t4, t5))));
//pxp[i][j] = MAX(pxp[i][j], MAX(t1, MAX(t2, MAX(t3, MAX(t4, MAX(t5, t6))))));
t1 = MAX(bu2[i-1][j-1], bd2[i-1][j-1]) + au_penalty(i,j) + retnucenergy(j); // closing bulge loop #ll
t2 = MAX(l1xn[i-1][j-1].score, lnx1[i-1][j-1].score) + tmatch2(i,j) + retnucenergy(j); //closing internal loop #mm
pxp[i][j] = MAX(pxp[i][j], MAX(t1, t2));
}
t1 = pxp[i-2][j] - MULTI_GAP_AFFINE - MULTI_GAP_PENALTY*2 + au_penalty(i-2,j); // closing (<7) s gap #nn
t2 = bu[i-1][j] - MULTI_GAP_PENALTY; // increasing length of (<7) s gap #oo
bu[i][j] = MAX(t1,t2);
//t1 = pxp[i-7][j] - MULTI_GAP_AFFINE_2 - MULTI_GAP_PENALTY_2; // closing (>6) s gap #pp
t1 = pxp[i-7][j] - MULTI_GAP_AFFINE_2 - MULTI_GAP_PENALTY_2 + au_penalty(i-7,j); // closing (>6) s gap #pp
t2 = bu2[i-1][j] - MULTI_GAP_PENALTY_2; // increasing length of (>6) s gap #qq
bu2[i][j] = MAX(t1, t2);
t1 = pxp[i][j-2] - MULTI_GAP_AFFINE - MULTI_GAP_PENALTY*2 + au_penalty(i,j-2) + affinePent(j-1,j); // closing (<7) t gap #rr
t2 = bd[i][j-1] - MULTI_GAP_PENALTY + retnucenergy(j); // increasing length of (<7) t gap #ss
bd[i][j] = MAX(t1, t2);
//t1 = pxp[i][j-7] - MULTI_GAP_AFFINE_2 - MULTI_GAP_PENALTY_2 + au_penalty(i,j-7) + 7*mean_pen;// closing (>6) t gap #tt
t1 = pxp[i][j-7] - MULTI_GAP_AFFINE_2 - MULTI_GAP_PENALTY_2 + au_penalty(i,j-7) + affinePent(j-6,j);// closing (>6) t gap #tt
t2 = bd2[i][j-1] - MULTI_GAP_PENALTY_2 + retnucenergy(j); // increasing length of (>6) t gap #uu
bd2[i][j] = MAX(t1, t2);
lu_policy(i, j, &lu[i][j]); // secondary structure restriction penalties now embedded in internal loop subs
ld_policy(i, j, &ld[i][j]);
l1xn_policy(i, j, &l1xn[i][j]);
lnx1_policy(i, j, &lnx1[i][j]);
//f[i][j] = pxp[i][j] + finalmatch(i,j);
f[i][j] = pxp[i-1][j-1] + finalmatch(i,j);
/*if((pxp[i][j] > 0) && !valid_pair(i-1,j-1))
printf("(%c,%c)",num_to_base(s[i-1]),num_to_base(t[j-1]));*/
}
}
}
/*
------------------------------- alignment ---------------------------
Do the traceback.
At each entry, figure out which matrix you come from.
pass it the starting location (i,j) and starting matrix, matrix_index
len_align is a global variable determining the current index of the alignment strings
*/
int alignment(const int i, const int j, const int matrix_index, const int prefill){
/*if((matrix_index == PXP_M) || (matrix_index == F_M)) {
//printf("%d,%d,%d,%c,%c\n",i-DUMMY_LENGTH,j-DUMMY_LENGTH,the_matrices[matrix_index][i][j],num_to_base(s[i-1]),num_to_base(t[j-1]));
printf("(%d,%d) Total: %d, Match: %d, Removal: %d [%c,%c]\n",i-DUMMY_LENGTH,j-DUMMY_LENGTH,the_matrices[matrix_index][i][j],match(i,j),affinePent(j,j),num_to_base(s[i-1]),num_to_base(t[j-1]));
}*/
//printf("matrix_index: %d, i:%d j:%d, G:%d\n", matrix_index,i-DUMMY_LENGTH,j-DUMMY_LENGTH, the_matrices[matrix_index][i][j]);
/*int mean_pen = 0; //removed 31 Oct 2011 by JH; use non-MFT Bindigo for oligo-oligo binding
if(len_t > PENALTY_THRESHOLD)
mean_pen = MEAN_PENALTY;*/
if( (i==DUMMY_LENGTH) && (j==DUMMY_LENGTH) ){
len_align = 0; //if you are here, the traceback is done
} else if( (i> DUMMY_LENGTH) && (j > DUMMY_LENGTH) && (matrix_index == PXP_M) ){
if( pxp[i][j] == pxp[i-1][j-1] + match(i,j) + affinePent(j,j)){ // #aa
alignment(i-1, j-1, PXP_M, prefill);
}
else if( pxp[i][j] == pxp[i-2][j-2] + i11(i,j) + affinePent(j-1,j)){ // #bb
alignment(i-2, j-2, PXP_M, prefill);
//printf("1x1: %d,%d\n",i-DUMMY_LENGTH,j-DUMMY_LENGTH);
if(prefill) {
len_align++;
aligned_s[len_align] = num_to_base(s[i-2]);
aligned_t[len_align] = num_to_base(t[j-2]);
}
}
else if( pxp[i][j] == pxp[i-2][j-3] + i12(i,j) + affinePent(j-2,j)){ // #cc
alignment(i-2, j-3, PXP_M, prefill);
//printf("1x2: %d,%d\n",i-DUMMY_LENGTH,j-DUMMY_LENGTH);
if(prefill) {
len_align++;
aligned_s[len_align] = '*';
aligned_t[len_align] = num_to_base(t[j-3]);
len_align++;
aligned_s[len_align] = num_to_base(s[i-2]);
aligned_t[len_align] = num_to_base(t[j-2]); // 09wkj CHANGED FROM j-3 to j-2, swapped *
}
}
else if( pxp[i][j] == pxp[i-3][j-2] + i21(i,j) + affinePent(j-1,j)){ // #dd
alignment(i-3, j-2, PXP_M, prefill);
//printf("2x1: %d,%d\n",i-DUMMY_LENGTH,j-DUMMY_LENGTH);
if(prefill) {
len_align++;
aligned_s[len_align] = num_to_base(s[i-3]);
aligned_t[len_align] = '*';
len_align++;
aligned_s[len_align] = num_to_base(s[i-2]); // 09wkj CHANGED FROM j-2 to i-2 4/20
aligned_t[len_align] = num_to_base(t[j-2]); // 09wkj CHANGED FROM j-3 to j-2, swapped *
}
}
else if( pxp[i][j] == pxp[i-3][j-3] + i22(i,j) + affinePent(j-2,j)){ // #ee
alignment(i-3, j-3, PXP_M, prefill);
//printf("2x2: %d,%d\n",i-DUMMY_LENGTH,j-DUMMY_LENGTH);
if(prefill) {
len_align++;
aligned_s[len_align] = num_to_base(s[i-3]);
aligned_t[len_align] = num_to_base(t[j-3]);
len_align++;
aligned_s[len_align] = num_to_base(s[i-2]);
aligned_t[len_align] = num_to_base(t[j-2]);
}
}
else if( pxp[i][j] == pxp[i-2][j-1] + matchAlt(i-2,i,j-1,j) - SINGLE_GAP_PENALTY + retnucenergy(j)){ // #ff
alignment(i-2, j-1, PXP_M, prefill);
//printf("s bulge: %d,%d\n",i-DUMMY_LENGTH,j-DUMMY_LENGTH);
if(prefill) {
len_align++;
aligned_s[len_align] = num_to_base(s[i-2]);
aligned_t[len_align] = '*';
}
}
else if( pxp[i][j] == pxp[i-1][j-2] + matchAlt(i-1,i,j-2,j) - SINGLE_GAP_PENALTY + affinePent(j-1,j)){ // #gg
//printf("t bulge: %d,%d\n",i-DUMMY_LENGTH,j-DUMMY_LENGTH);
alignment(i-1, j-2, PXP_M, prefill);
if(prefill) {
len_align++;
aligned_s[len_align] = '*';
aligned_t[len_align] = num_to_base(t[j-2]);
}
}
else if( pxp[i][j] == bu[i-1][j-1] + au_penalty(i,j) + retnucenergy(j)){ // #hh
alignment(i-1, j-1, BU_M, prefill);
}
else if( pxp[i][j] == bd[i-1][j-1] + au_penalty(i,j) + retnucenergy(j)){ // #ii
//printf("%d %d ??\n",i,j);
alignment(i-1, j-1, BD_M, prefill);
}
else if( pxp[i][j] == bu2[i-1][j-1] + au_penalty(i,j) + retnucenergy(j)){ // #ll (1/2)
alignment(i-1, j-1, BU2_M, prefill);
}
else if( pxp[i][j] == bd2[i-1][j-1] + au_penalty(i,j) + retnucenergy(j)){ // #ll (2/2)
alignment(i-1, j-1, BD2_M, prefill);
}
else if( pxp[i][j] == l1xn[i-1][j-1].score + tmatch2(i,j) + retnucenergy(j)){ // #mm (1/2)
//printf(" in l1xn \n");
alignment(i-l1xn[i-1][j-1].up-1, j-l1xn[i-1][j-1].down-1, PXP_M, prefill);
if(prefill)
bigfill(i,j, l1xn[i-1][j-1].up, l1xn[i-1][j-1].down);
}
else if( pxp[i][j] == lnx1[i-1][j-1].score + tmatch2(i,j) + retnucenergy(j)){ // #mm (2/2)
//printf(" in lnx1 \n");
alignment(i-lnx1[i-1][j-1].up-1, j-lnx1[i-1][j-1].down-1, PXP_M, prefill);
if(prefill)
bigfill(i,j, lnx1[i-1][j-1].up, lnx1[i-1][j-1].down);
}
else if( pxp[i][j] == lu[i-1][j-1].score + tmatch2(i,j) + retnucenergy(j)){ // #jj
//printf(" in lu \n");
alignment(i-lu[i-1][j-1].up-1, j-lu[i-1][j-1].down-1, PXP_M, prefill);
if(prefill)
bigfill(i,j, lu[i-1][j-1].up, lu[i-1][j-1].down);
}
else if( pxp[i][j] == ld[i-1][j-1].score + tmatch2(i,j) + retnucenergy(j)){ // #kk
//printf("%d,%d in ld \n",i-DUMMY_LENGTH,j-DUMMY_LENGTH);
alignment(i-ld[i-1][j-1].up-1, j-ld[i-1][j-1].down-1, PXP_M, prefill);
if(prefill)
bigfill(i,j, ld[i-1][j-1].up, ld[i-1][j-1].down);
} else { //end of alignment.
//printf("prefix fill: %d,%d\n",i-DUMMY_LENGTH-1,j-DUMMY_LENGTH-1);
//len_align = 0;
if(prefill) {
fill_prefix(i-1,j-1);
}
}
//printf("(m:%d f:%d)[i: %c j:%c]",firstcomp(s[i-1],t[j-1]),prefill,num_to_base(s[i-1]),num_to_base(t[j-1]));
//printf("(m:%d f:%d)[i: %d j:%d]",firstcomp(s[i-1],t[j-1]),prefill,s[i-1],t[j-1]);
//printf("paired: %d,%d @ %d\n",i-DUMMY_LENGTH,j-DUMMY_LENGTH,f[i+1][j+1]);
if(prefill) {
len_align++;
aligned_s[len_align] = tolower(num_to_base(s[i-1]));
aligned_t[len_align] = tolower(num_to_base(t[j-1]));
}
pairs[i-DUMMY_LENGTH-1][j-DUMMY_LENGTH-1] = paired;
if(!prefill) {
if(f[f_i][f_j] > dgJ[j - DUMMY_LENGTH - 1]) {
dgJ[j - DUMMY_LENGTH - 1] = f[f_i][f_j];
}
}
} else if ( (i > DUMMY_LENGTH) && (j > DUMMY_LENGTH ) && (matrix_index == BU_M) ){
if( bu[i][j] == pxp[i-2][j] - MULTI_GAP_AFFINE - MULTI_GAP_PENALTY*2 + au_penalty(i-2,j) ){ // #nn
alignment(i-2, j, PXP_M,prefill);
if(prefill) {
len_align++;
aligned_s[len_align] = num_to_base( s[i-2] );
aligned_t[len_align] = '*';
len_align++;
aligned_s[len_align] = num_to_base( s[i-1] );
aligned_t[len_align] = '*';
}
}
else if( bu[i][j] == bu[i-1][j] - MULTI_GAP_PENALTY){ // #oo
alignment(i-1, j, BU_M,prefill);
if(prefill) {
len_align++;
aligned_s[len_align] = num_to_base( s[i-1] );
aligned_t[len_align] = '*';
}
}
}
else if ( (i > DUMMY_LENGTH) && (j > DUMMY_LENGTH ) && (matrix_index == BD_M) ){
if( bd[i][j] == pxp[i][j-2] - MULTI_GAP_AFFINE - MULTI_GAP_PENALTY*2 + au_penalty(i,j-2) + affinePent(j-1,j) ){ // #rr
//printf("%d,%d !?\n",i,j);
alignment(i, j-2, PXP_M, prefill);
if(prefill) {
len_align++;
aligned_s[len_align] = '*';
aligned_t[len_align] = num_to_base( t[j-2] );
len_align++;
aligned_s[len_align] = '*';
aligned_t[len_align] = num_to_base( t[j-1] );
}
}
else if( bd[i][j] == bd[i][j-1] - MULTI_GAP_PENALTY + retnucenergy(j)){ // #ss
//printf("%d,%d !\n",i,j);
alignment(i, j-1, BD_M, prefill);
if(prefill) {
len_align++;
aligned_s[len_align] = '*';
aligned_t[len_align] = num_to_base( t[j-1] );
}
}
}
else if ( (i > DUMMY_LENGTH) && (j > DUMMY_LENGTH ) && (matrix_index == BU2_M) ){
if( bu2[i][j] == pxp[i-7][j] - MULTI_GAP_AFFINE_2 - MULTI_GAP_PENALTY_2 + au_penalty(i-7,j) ){ // #pp
int ii;
alignment(i-7, j, PXP_M, prefill);
//bigfill(i,j,7,0);
if(prefill) {
for(ii = 7; ii > 0; --ii){
len_align++;
aligned_s[len_align] = num_to_base( s[i-ii] );
aligned_t[len_align] = '*';
}
}
}
else if( bu2[i][j] == bu2[i-1][j] - MULTI_GAP_PENALTY_2){ // #qq
alignment(i-1, j, BU2_M, prefill);
if(prefill) {
len_align++;
aligned_s[len_align] = num_to_base( s[i-1] );
aligned_t[len_align] = '*';
}
}
}
else if ( (i > DUMMY_LENGTH) && (j > DUMMY_LENGTH ) && (matrix_index == BD2_M) ){
if( bd2[i][j] == pxp[i][j-7] - MULTI_GAP_AFFINE_2 - MULTI_GAP_PENALTY_2 + au_penalty(i,j-7) + affinePent(j-6,j)){ // #tt
int jj;
alignment(i, j-7, PXP_M, prefill);
//bigfill(i,j,0,7);
if(prefill) {
for(jj = 7; jj > 0; --jj){
len_align++;
aligned_s[len_align] = '*';
aligned_t[len_align] = num_to_base( t[j-jj] );
}
}
}
else if( bd2[i][j] == bd2[i][j-1] - MULTI_GAP_PENALTY_2 + retnucenergy(j)){ // #uu
alignment(i, j-1, BD2_M, prefill);
if(prefill) {
len_align++;
aligned_s[len_align] = '*';
aligned_t[len_align] = num_to_base( t[j-1] );
}
}
}
else if( (i > DUMMY_LENGTH) && (j > DUMMY_LENGTH) && (matrix_index == F_M) ){
if( f[i][j] == pxp[i-1][j-1] + finalmatch(i,j) ){// + mean_pen){ // #vv
alignment(i-1,j-1, PXP_M, prefill);
if(prefill)
len_align++;
}
} else { //end of alignment
//printf("not paired: %d,%d\n",i-DUMMY_LENGTH-1,j-DUMMY_LENGTH-1);
len_align = 0;
//fill in the beginning of the strings
if(prefill) { //if we are only interested in o(j), then no prefix fill.
fill_prefix(i,j);
}
}
return 0;
}
int valid_pair(int i,int j) {
if((s[i] == 0) && (t[j] == 3)) {
return 1;
} else if((s[i] == 3) && (t[j] == 0)) {
return 1;
} else if((s[i] == 1) && (t[j] == 2)) {
return 1;
} else if((s[i] == 2) && (t[j] == 1)) {
return 1;
} else if((s[i] == 2) && (t[j] == 3)) {
return 1;
} else if((s[i] == 3) && (t[j] == 2)) {
return 1;
} else {
return 0;
}
}
//In this case, we only wish to perform the traceback and output which sites are paired, rather than print a formatted string.
//int traceback(const int i, const int j, const int matrix_index){
//
// //printf("matrix_index: %d, i:%d j:%d, G:%d\n", matrix_index,i-DUMMY_LENGTH,j-DUMMY_LENGTH, the_matrices[matrix_index][i][j]);
// /*int mean_pen = 0; //removed 31 Oct 2011 by JH; use non-MFT Bindigo for oligo-oligo binding
// if(len_t > PENALTY_THRESHOLD)
// mean_pen = MEAN_PENALTY;*/
//
// if( (i==DUMMY_LENGTH) && (j==DUMMY_LENGTH) ){
// len_align = 0; //if you are here, the traceback is done
// }
// else if( (i> DUMMY_LENGTH) && (j > DUMMY_LENGTH) && (matrix_index == PXP_M) ){
//
// if( pxp[i][j] == pxp[i-1][j-1] + match(i,j) + retnucenergy(j)){ // #aa
//
// traceback(i-1, j-1, PXP_M);
//
// }
// else if( pxp[i][j] == pxp[i-2][j-2] + i11(i,j) + affinePent(j-1,j)){ // #bb
//
// traceback(i-2, j-2, PXP_M);
//
// len_align++;
// aligned_sB[len_align] = num_to_base(s[i-2]);
// aligned_tB[len_align] = num_to_base(t[j-2]);
// }
// else if( pxp[i][j] == pxp[i-2][j-3] + i12(i,j) + affinePent(j-2,j)){ // #cc
// traceback(i-2, j-3, PXP_M);
//
// len_align++;
// aligned_sB[len_align] = '*';
// aligned_tB[len_align] = num_to_base(t[j-3]);
//
// len_align++;
//
// aligned_sB[len_align] = num_to_base(s[i-2]);
// aligned_tB[len_align] = num_to_base(t[j-2]); // 09wkj CHANGED FROM j-3 to j-2, swapped *
// }
// else if( pxp[i][j] == pxp[i-3][j-2] + i21(i,j) + affinePent(j-1,j)){ // #dd
// traceback(i-3, j-2, PXP_M);
//
// len_align++;
// aligned_sB[len_align] = num_to_base(s[i-3]);
// aligned_tB[len_align] = '*';
//
// len_align++;
// aligned_sB[len_align] = num_to_base(s[i-2]); // 09wkj CHANGED FROM j-2 to i-2 4/20
// aligned_tB[len_align] = num_to_base(t[j-2]); // 09wkj CHANGED FROM j-3 to j-2, swapped *
// }
// else if( pxp[i][j] == pxp[i-3][j-3] + i22(i,j) + affinePent(j-2,j)){ // #ee
// traceback(i-3, j-3, PXP_M);
//
// len_align++;
// aligned_sB[len_align] = num_to_base(s[i-3]);
// aligned_tB[len_align] = num_to_base(t[j-3]);
//
// len_align++;
// aligned_sB[len_align] = num_to_base(s[i-2]);
// aligned_tB[len_align] = num_to_base(t[j-2]);
// }
// else if( pxp[i][j] == pxp[i-2][j-1] + matchAlt(i-2,i,j-1,j) - SINGLE_GAP_PENALTY + retnucenergy(j)){ // #ff
// traceback(i-2, j-1, PXP_M);
//
// len_align++;
// aligned_sB[len_align] = num_to_base(s[i-2]);
// aligned_tB[len_align] = '*';
//
// }
// else if( pxp[i][j] == pxp[i-1][j-2] + matchAlt(i-1,i,j-2,j) - SINGLE_GAP_PENALTY + affinePent(j-1,j)){ // #gg
// traceback(i-1, j-2, PXP_M);
//
// len_align++;
// aligned_sB[len_align] = '*';
// aligned_tB[len_align] = num_to_base(t[j-2]);
//
// }
// else if( pxp[i][j] == bu[i-1][j-1] + au_penalty(i,j) + retnucenergy(j)){ // #hh
// traceback(i-1, j-1, BU_M);
// }
// else if( pxp[i][j] == bd[i-1][j-1] + au_penalty(i,j) + retnucenergy(j)){ // #ii
// traceback(i-1, j-1, BD_M);
// }
// else if( pxp[i][j] == bu2[i-1][j-1] + au_penalty(i,j) + retnucenergy(j)){ // #ll (1/2)
// traceback(i-1, j-1, BU2_M);
// }
// else if( pxp[i][j] == bd2[i-1][j-1] + au_penalty(i,j) + retnucenergy(j)){ // #ll (2/2)
// traceback(i-1, j-1, BD2_M);
// }
// else if( pxp[i][j] == l1xn[i-1][j-1].score + tmatch2(i,j) + retnucenergy(j)){ // #mm (1/2)
// printf(" in l1xn \n");
// traceback(i-l1xn[i-1][j-1].up-1, j-l1xn[i-1][j-1].down-1, PXP_M);
//
// bigfill(i,j, l1xn[i-1][j-1].up, l1xn[i-1][j-1].down);
// }
// else if( pxp[i][j] == lnx1[i-1][j-1].score + tmatch2(i,j) + retnucenergy(j)){ // #mm (2/2)
// printf(" in lnx1 \n");
//
// traceback(i-lnx1[i-1][j-1].up-1, j-lnx1[i-1][j-1].down-1, PXP_M);
// bigfill(i,j, lnx1[i-1][j-1].up, lnx1[i-1][j-1].down);
// }
// else if( pxp[i][j] == lu[i-1][j-1].score + tmatch2(i,j) + retnucenergy(j)){ // #jj
// printf(" in lu \n");
// traceback(i-lu[i-1][j-1].up-1, j-lu[i-1][j-1].down-1, PXP_M);
//
// bigfill(i,j, lu[i-1][j-1].up, lu[i-1][j-1].down);
// }
// else if( pxp[i][j] == ld[i-1][j-1].score + tmatch2(i,j) + retnucenergy(j)){ // #kk
// printf(" in ld \n");
//
// traceback(i-ld[i-1][j-1].up-1, j-ld[i-1][j-1].down-1, PXP_M);
// bigfill(i,j, ld[i-1][j-1].up, ld[i-1][j-1].down);
// }
// else { // TODO anything here?
// fill_prefix(i-1,j-1);
// }
// len_align++;
// aligned_sB[len_align] = tolower(num_to_base(s[i-1]));
// aligned_tB[len_align] = tolower(num_to_base(t[j-1]));
//
// pairs[i-DUMMY_LENGTH-1][j-DUMMY_LENGTH-1] = paired;
//
// // pairs[len_align-1] = '|';
// // aligned_sB[len_align+1] = num_to_base(s[i]);
// //aligned_tB[len_align+1] = num_to_base(t[j]);
//
// }
// else if ( (i > DUMMY_LENGTH) && (j > DUMMY_LENGTH ) && (matrix_index == BU_M) ){
//
// if( bu[i][j] == pxp[i-2][j] - MULTI_GAP_AFFINE - MULTI_GAP_PENALTY*2 + au_penalty(i-2,j) ){ // #nn
// traceback(i-2, j, PXP_M);
//
// len_align++;
// aligned_sB[len_align] = num_to_base( s[i-2] );
// aligned_tB[len_align] = '*';
//
// len_align++;
// aligned_sB[len_align] = num_to_base( s[i-1] );
// aligned_tB[len_align] = '*';
// }
// else if( bu[i][j] == bu[i-1][j] - MULTI_GAP_PENALTY){ // #oo
// traceback(i-1, j, BU_M);
//
// len_align++;
// aligned_sB[len_align] = num_to_base( s[i-1] );
// aligned_tB[len_align] = '*';
// }
// }
// else if ( (i > DUMMY_LENGTH) && (j > DUMMY_LENGTH ) && (matrix_index == BD_M) ){
//
// if( bd[i][j] == pxp[i][j-2] - MULTI_GAP_AFFINE - MULTI_GAP_PENALTY*2 + au_penalty(i,j-2) + affinePent(j-1,j) ){ // #rr
// traceback(i, j-2, PXP_M);
//
// len_align++;
// aligned_sB[len_align] = '*';
// aligned_tB[len_align] = num_to_base( t[j-2] );
//
// len_align++;
// aligned_sB[len_align] = '*';
// aligned_tB[len_align] = num_to_base( t[j-1] );
//
// }
// else if( bd[i][j] == bd[i][j-1] - MULTI_GAP_PENALTY + retnucenergy(j)){ // #ss
// traceback(i, j-1, BD_M);
//
// len_align++;
// aligned_sB[len_align] = '*';
// aligned_tB[len_align] = num_to_base( t[j-1] );
// }
// }
// else if ( (i > DUMMY_LENGTH) && (j > DUMMY_LENGTH ) && (matrix_index == BU2_M) ){
//
// if( bu2[i][j] == pxp[i-7][j] - MULTI_GAP_AFFINE_2 - MULTI_GAP_PENALTY_2 + au_penalty(i-7,j) + affinePent(j-6,j) ){ // #pp
// int ii;
// traceback(i-7, j, PXP_M);
//
// //bigfill(i,j,7,0);
// for(ii = 7; ii > 0; --ii){
// len_align++;
// aligned_sB[len_align] = num_to_base( s[i-ii] );
// aligned_tB[len_align] = '*';
// }
// }
// else if( bu2[i][j] == bu2[i-1][j] - MULTI_GAP_PENALTY_2){ // #qq
// traceback(i-1, j, BU2_M);
// len_align++;
// aligned_sB[len_align] = num_to_base( s[i-1] );
// aligned_tB[len_align] = '*';
// }
// }
// else if ( (i > DUMMY_LENGTH) && (j > DUMMY_LENGTH ) && (matrix_index == BD2_M) ){
//
// if( bd2[i][j] == pxp[i][j-7] - MULTI_GAP_AFFINE_2 - MULTI_GAP_PENALTY_2 + au_penalty(i,j-7) + retnucenergy(j)){ // #tt
// int jj;
// traceback(i, j-7, PXP_M);
//
// //bigfill(i,j,0,7);
// for(jj = 7; jj > 0; --jj){
// len_align++;
// aligned_sB[len_align] = '*';
// aligned_tB[len_align] = num_to_base( t[j-jj] );
// }
//
// }
// else if( bd2[i][j] == bd2[i][j-1] - MULTI_GAP_PENALTY_2 + retnucenergy(j)){ // #uu
// traceback(i, j-1, BD2_M);
// len_align++;
// aligned_sB[len_align] = '*';
// aligned_tB[len_align] = num_to_base( t[j-1] );
// }
// }
//
// else if( (i > DUMMY_LENGTH) && (j > DUMMY_LENGTH) && (matrix_index == F_M) ){
//
// if( f[i][j] == pxp[i-1][j-1] + finalmatch(i,j) ){// + mean_pen){ // #vv
// traceback(i-1,j-1, PXP_M);
//
// len_align++;
// }
// }
// else {
// len_align = 0;
//
// //fill in the beginning of the strings
// fill_prefix(i,j);
//
// }
//
// return 0;
//}
void fill_prefix(const int i, const int j ){
int max_prefix = MAX(i,j); //fill in the longest prefix first
int x;
// printf( "i: %d, j: %d\n", i, j);
if( max_prefix == i ){
for( x = DUMMY_LENGTH; x < i; x++ )
aligned_s[x] = num_to_base(s[x]);
for( x = DUMMY_LENGTH; x < j; x++ )
aligned_t[ x + i - j] = num_to_base(t[x]);
len_align = max_prefix - 1;
} else {
for( x = DUMMY_LENGTH; x < j; x++ )
aligned_t[x] = num_to_base(t[x]);
for( x = DUMMY_LENGTH; x < i; x++ )
aligned_s[ x + j - i] = num_to_base(s[x]);
len_align = max_prefix - 1;
}
}
//convert the sequence code number to the corresponding character
char num_to_base(const int i) {
return code[i];
}
//return filename concatenated with the path
void stackstrcat(char * str, char * dest) {
char * env = getenv("BINPATH");
char buf[strlen(env) + strlen(str) + 1];
strcpy(buf,env);
if(env[strlen(env) - 1] != '/')
strcat(buf,"/");
strcat(buf,str);
strcpy(dest,buf);
}
/*
scan in the files, parse the data files and fill the array.
*/
void get_stack_energies() {
int temp, i, j;
int count = 6*6*6*6; // stack, tstack, and tstacki all 6*6*6*6 ints
/*
read stack data files
*/
FILE *filestack, *filetstack, *filetstacki;
char * wd = getenv("BINPATH");
if(wd != NULL) {
char * path = malloc(strlen(wd) + 20);
stackstrcat(BINPREFIX "stack.bin",path);
filestack = fopen(path,"r");
if(filestack != NULL) {
temp = fread(&stack_energy, sizeof(int), count, filestack);
if(temp != count)
printf("Only wrote %d elements of stack\n",temp);
fclose(filestack);
} else {
printf("Could not open stacking binary (stack.bin) for reading!\n");
exit(1);
}
stackstrcat(BINPREFIX "tstack.bin",path);
filetstack = fopen(path,"r");
if(filetstack != NULL) {
temp = fread(&tstack_energy, sizeof(int), 6*6*6*6, filetstack);
if(temp != count)
printf("Only wrote %d elements of tstack\n",temp);
fclose(filetstack);
} else {
printf("Could not open terminal stack binary (tstack.bin) for reading!\n");
exit(1);
}
stackstrcat(BINPREFIX "tstacki.bin",path);
filetstacki = fopen(path,"r");
if(filetstacki != NULL) {
temp = fread(&tstacki_energy, sizeof(int), 6*6*6*6, filetstacki);
if(temp != count)
printf("Only wrote %d elements of tstacki\n",temp);
fclose(filetstacki);
} else {
printf("Could not open internal loop terminal stack binary (tstacki.bin) for reading!\n");
exit(1);
}
//TODO: understand this.
for( i = 1; i < 5; i++ ){
for( j = 1; j < 5; j++){
tstack_energy[i][j][5][5] = 0;
tstack_energy[5][5][i][j] = 0;
}
}
free(path);
} else {
printf("Thermodynamic datatable directory environment variable not set. Please run export BINPATH=\"/path/to/datatables/\"\n");
exit(1);
}
}
/*
fill the energy arrays for the internal loops by opening the files containing the binary memory images
*/
void get_iloop_energies(){
int temp, count;
FILE* file1x1, *file2x2, *file2x1;
char * wd = getenv("BINPATH");
if(wd != NULL) {
char * path = malloc(strlen(wd) + 20);
stackstrcat(BINPREFIX "int1x1.bin",path);
file1x1 = fopen(path,"r");
if(file1x1 != NULL) {
count = 6*6*6*6*6*6; //1x1 is 6*6*6*6*6*6 ints
temp = fread(&iloop11, sizeof(int), count, file1x1);
if(temp != count)
printf("Only wrote %d elements of 1x1\n",temp);
fclose(file1x1);
} else {
printf("Could not open internal 1x1 loop binary (int1x1.bin) for reading!\n");
exit(1);
}
stackstrcat(BINPREFIX "int2x2.bin",path);
file2x2 = fopen(path,"r");
if(file2x2 != NULL) {
count = 6*6*6*6*6*6*6*6; //2x2 is 6*6*6*6*6*6*6*6 ints
temp = fread(&iloop22, sizeof(int), count, file2x2);
if(temp != count)
printf("Only wrote %d elements of 2x2\n",temp);
fclose(file2x2);
} else {
printf("Could not open internal 2x2 loop binary (int2x2.bin) for reading!\n");