PUBLIC float profile_aln(const float *T1, const char *seq1,
const float *T2, const char *seq2)
{
/* align the 2 probability profiles T1, T2 */
/* This is like a Needleman-Wunsch alignment, with affine gap-costs
ala Gotoh. The score looks at both seq and pair profile */
float **S, **E, **F, tot_score=0.;
int i, j, length1, length2;
length1 = strlen(seq1);
length2 = strlen(seq2);
S = newmat(length1, length2);
E = newmat(length1, length2);
F = newmat(length1, length2);
E[0][0] = F[0][0] = open - ext;
S[0][0] = 0;
for (i=1; i<=length1; i++) F[i][0] = -9999; /* impossible */
for (j=1; j<=length2; j++) E[0][j] = -9999; /* impossible */
if (!free_ends) {
for (i=1; i<=length1; i++) S[i][0] = E[i][0] = E[i-1][0] +ext;
for (j=1; j<=length2; j++) S[0][j] = F[0][j] = F[0][j-1] +ext;
}
for (i=1; i<=length1; i++) {
for (j=1; j<=length2; j++) {
float M;
E[i][j] = eMAX(E[i-1][j]+ext, S[i-1][j]+open);
F[i][j] = eMAX(F[i][j-1]+ext, S[i][j-1]+open);
M = S[i-1][j-1] + PrfEditScore(T1+3*i,T2+3*j, seq1[i-1], seq2[j-1]);
S[i][j] = MAX3(M, E[i][j], F[i][j]);
}
}
if (edit_backtrack) {
double score=0;
char state = 'S';
int pos, i,j;
alignment[0] = (int *) space((length1+length2+1)*sizeof(int));
alignment[1] = (int *) space((length1+length2+1)*sizeof(int));
pos = length1+length2;
i = length1;
j = length2;
tot_score = S[length1][length2];
if (free_ends) {
/* find starting point for backtracking,
search for highest entry in last row or column */
int imax=0;
for (i=1; i<=length1; i++) {
if (S[i][length2]>score) {
score=S[i][length2];
imax=i;
}
}
for (j=1; j<=length2; j++) {
if (S[length1][j]>score) {
score=S[length1][j];
imax=-j;
}
}
if (imax<0) {
for (j=length2; j> -imax; j--) {
alignment[0][pos] = 0;
alignment[1][pos--] = j;
}
i=length1;
} else {
for (i=length1; i>imax; i--) {
alignment[0][pos] = i;
alignment[1][pos--] = 0;
}
j=length2;
}
tot_score=score;
}
while (i>0 && j>0) {
switch (state) {
case 'E':
score = E[i][j];
alignment[0][pos] = i;
alignment[1][pos--] = 0;
if (EQUAL(score, S[i-1][j] + open)) state = 'S';
i--;
break;
case 'F':
score = F[i][j];
alignment[0][pos] = 0;
alignment[1][pos--] = j;
if (EQUAL(score, S[i][j-1] + open)) state = 'S';
j--;
break;
case 'S':
score = S[i][j];
if (EQUAL(score, E[i][j])) state = 'E';
else if (EQUAL(score, F[i][j])) state = 'F';
else if (EQUAL(score, S[i-1][j-1] +
PrfEditScore(T1+3*i,T2+3*j, seq1[i-1], seq2[j-1]))) {
alignment[0][pos] = i;
alignment[1][pos--] = j;
i--; j--;
}
else nrerror("backtrack of alignment failed");
break;
}
}
for (; j>0; j--) {
alignment[0][pos] = 0;
alignment[1][pos--] = j;
}
for (; i>0; i--) {
alignment[0][pos] = i;
alignment[1][pos--] = 0;
}
for(i=pos+1; i<=length1+length2; i++){
alignment[0][i-pos] = alignment[0][i];
alignment[1][i-pos] = alignment[1][i];
}
alignment[0][0] = length1+length2-pos; /* length of alignment */
sprint_aligned_bppm(T1,seq1, T2,seq2);
free(alignment[0]);
free(alignment[1]);
}
for (i=0; i<=length1; i++) {
free(S[i]); free(E[i]); free(F[i]);
}
free(S); free(E); free(F);
return tot_score;
}
PUBLIC float profile_edit_distance(const float *T1, const float *T2)
{
/* align the 2 probability profiles T1, T2 */
/* This is like a Needleman-Wunsch alignment,
we should really use affine gap-costs ala Gotoh */
float **distance;
short **i_point, **j_point;
int i, j, i1, j1, pos, length1,length2;
float minus, plus, change, temp;
length1 = (int) T1[0];
length2 = (int) T2[0];
distance = (float **) vrna_alloc((length1 +1)*sizeof(float *));
if(edit_backtrack){
i_point = (short **) vrna_alloc((length1 +1)*sizeof(short *));
j_point = (short **) vrna_alloc((length1 +1)*sizeof(short *));
}
for(i=0; i<= length1; i++){
distance[i] = (float *) vrna_alloc( (length2+1)*sizeof(float));
if(edit_backtrack){
i_point[i] = (short *) vrna_alloc( (length2+1)*sizeof(short));
j_point[i] = (short *) vrna_alloc( (length2+1)*sizeof(short));
}
}
for(i = 1; i <= length1; i++) {
distance[i][0] = distance[i-1][0]+PrfEditCost(i,0,T1,T2);
if(edit_backtrack){ i_point[i][0] = (short) i-1; j_point[i][0] = 0; }
}
for(j = 1; j <= length2; j++) {
distance[0][j] = distance[0][j-1]+PrfEditCost(0,j,T1,T2);
if(edit_backtrack){ i_point[0][j] = 0; j_point[0][j] = (short) j-1; }
}
for (i = 1; i <= length1; i++) {
for (j = 1; j <= length2 ; j++) {
minus = distance[i-1][j] + PrfEditCost(i,0,T1,T2);
plus = distance[i][j-1] + PrfEditCost(0,j,T1,T2);
change = distance[i-1][j-1]+ PrfEditCost(i,j,T1,T2);
distance[i][j] = MIN3(minus, plus, change);
/* printf("%g ", distance[i][j]); */
if(edit_backtrack){
if(distance[i][j] == change) {
i_point[i][j]= (short)i-1; j_point[i][j]= (short) j-1; }
else if(distance[i][j] == plus) {
i_point[i][j]= (short)i ; j_point[i][j]= (short)j-1; }
else {
i_point[i][j]= (short)i-1; j_point[i][j]= (short)j ; }
}
}
/* printf("\n"); */
}
/* printf("\n"); */
temp = distance[length1][length2];
for(i=0;i<=length1;i++)
free(distance[i]);
free(distance);
if(edit_backtrack){
alignment[0] = (int *) vrna_alloc((length1+length2+1)*sizeof(int));
alignment[1] = (int *) vrna_alloc((length1+length2+1)*sizeof(int));
pos = length1+length2;
i = length1;
j = length2;
while( (i>0)||(j>0) ) {
i1 = i_point[i][j];
j1 = j_point[i][j];
if( ((i-i1)==1)&&((j-j1)==1) ) { /* substitution */
alignment[0][pos] = i;
alignment[1][pos] = j;
}
if( ((i-i1)==1)&&(j==j1) ) { /* Deletion in [1] */
alignment[0][pos] = i;
alignment[1][pos] = 0;
}
if( (i==i1)&&((j-j1)==1) ) { /* Deletion in [0] */
alignment[0][pos] = 0;
alignment[1][pos] = j;
}
pos--;
i = i1;
j = j1;
}
for(i=pos+1; i<=length1+length2; i++){
alignment[0][i-pos] = alignment[0][i];
alignment[1][i-pos] = alignment[1][i];
}
alignment[0][0] = length1+length2-pos; /* length of alignment */
for(i=0; i<=length1; i++){
free(i_point[i]); free(j_point[i]);
}
free(i_point); free(j_point);
sprint_aligned_bppm(T1,T2);
free(alignment[0]);
free(alignment[1]);
}
return temp;
}
