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/****************************************************************************
*
* Copyright (c) 2003, The Institute for Genomic Research (TIGR), Rockville,
* Maryland, U.S.A. All rights reserved.
*
****************************************************************************/
#define VERYBAD 16
static struct stack_struct {
int i, j, m, c;
} stack[100];
static int abi_size=16;
static unsigned abi_mask;
struct abi_struct {
unsigned tag;
int index;
} *abi_well;
struct hit_struct {
int diff, count;
} *hit_well;
static condition[]={
-1, -1, -1, -1, -1, -1, -1, -1, -1, 0, /* 0-19 */
0, 0, 0, 0, 0, 0, 0, 0, 0, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, /* 20-39 */
3, 3, 3, 3, 3, 3, 3, 3, 3, 6,
6, 6, 6, 6, 6, 6, 6, 6, 6, 6, /* 40-59 */
6, 6, 6, 6, 6, 6, 6, 6, 6, 9,
9, 9, 9, 9, 9, 9, 9, 9, 9, 9, /* 60-79 */
9, 9, 9, 9, 9, 9, 9, 9, 9, 12,
12, 12, 12, 12, 12, 12, 12, 12, 12, 12, /* 80-99 */
12, 12, 12, 12, 12, 12, 12, 12, 12, 15};
static int badness[16][16]= {
/* A C G T U R Y M W S K D H V B N */
/*A*/ { 0, 3, 3, 3, 3, 1, 3, 1, 1, 3, 3, 1, 1, 1, 3, 2},
/*C*/ { 3, 0, 3, 3, 3, 3, 1, 1, 3, 1, 3, 3, 1, 1, 1, 2},
/*G*/ { 3, 3, 0, 3, 3, 1, 3, 3, 3, 1, 1, 1, 3, 1, 1, 2},
/*T*/ { 3, 3, 3, 0, 0, 3, 1, 3, 1, 3, 1, 1, 1, 3, 1, 2},
/*U*/ { 3, 3, 3, 0, 0, 3, 1, 3, 1, 3, 1, 1, 1, 3, 1, 2},
/*R*/ { 1, 3, 1, 3, 3, 1, 3, 2, 2, 2, 2, 2, 3, 2, 3, 3},
/*Y*/ { 3, 1, 3, 1, 1, 3, 1, 2, 2, 2, 2, 3, 2, 3, 2, 3},
/*M*/ { 1, 1, 3, 3, 3, 2, 2, 1, 2, 2, 3, 3, 2, 2, 3, 3},
/*W*/ { 1, 3, 3, 1, 1, 2, 2, 2, 1, 3, 2, 2, 2, 3, 3, 3},
/*S*/ { 3, 1, 1, 3, 3, 2, 2, 2, 3, 1, 2, 3, 3, 2, 2, 3},
/*K*/ { 3, 3, 1, 1, 1, 2, 2, 3, 2, 2, 1, 2, 3, 3, 2, 3},
/*D*/ { 1, 3, 1, 1, 1, 2, 3, 3, 2, 3, 2, 2, 3, 3, 3, 3},
/*H*/ { 1, 1, 3, 1, 1, 3, 2, 2, 2, 3, 3, 3, 2, 3, 3, 3},
/*V*/ { 1, 1, 1, 3, 3, 2, 3, 2, 3, 2, 3, 3, 3, 2, 3, 3},
/*B*/ { 3, 1, 1, 1, 1, 3, 2, 3, 3, 2, 2, 3, 3, 3, 2, 3},
/*N*/ { 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3},
/* A C G T U R Y M W S K D H V B N */
};
static int Dlist[]={ 0, 2, 3}, Hlist[]={ 0, 1, 3};
int abi_code(c)
int c;
{
register int tmp;
switch (c) {
case 0: tmp=0; break;
case 1: tmp=1; break;
case 2: tmp=2; break;
case 3:
case 4: tmp=3; break;
case 5: tmp=random()%2 ? 2 : 0; break;
case 6: tmp=random()%2 ? 3 : 1; break;
case 7: tmp=random()%2 ; break;
case 8: tmp=random()%2 ? 3 : 0; break;
case 9: tmp=random()%2 ? 2 : 1; break;
case 10: tmp=random()%2 ? 3 : 2; break;
case 11: tmp=Dlist[random()%3]; break;
case 12: tmp=Hlist[random()%3]; break;
case 13: tmp=random()%3; break;
case 14: tmp=random()%3+1; break;
case 15: tmp=random()%4; break;
default:
giveup("how can other cases happen in tag_code?");
}
return tmp;
}
void abi_sort(l, r)
struct abi_struct *l, *r;
{
register unsigned v;
register struct abi_struct *i, *j, tmp;
if (r>l) {
v = r->tag; i = l-1; j = r;
while (1) {
while ((++i)->tag < v) ;
while (j>l && (--j)->tag > v) ;
if (i>=j) break;
tmp = *i; *i = *j; *j = tmp;
}
tmp = *i; *i = *r; *r = tmp;
abi_sort(l, i-1);
abi_sort(i+1, r);
}
}
void prepare_abi_mask()
{
register int i;
register unsigned acc;
/* construct abi_mask */
for (acc=i=0; i<abi_size; i++) {
acc<<=2;
acc|=3;
}
abi_mask=acc;
}
void abi_align(a, width, b, height, start, end)
char *a, *b;
int width, height;
int *start, *end;
{
register int i, j, l, r, m, diff, count;
register unsigned x;
int left, span, abi_len, hit_len;
/* construct 'a' sequence tags */
for (x=i=0; i<abi_size-1; i++, x<<=2)
x|=abi_code(a[i]);
for (j=0; i<width; i++, j++, x<<=2) {
x|=abi_code(a[i]);
x&=abi_mask;
abi_well[j].tag=x;
abi_well[j].index=i;
}
abi_len=j;
abi_sort(abi_well, &abi_well[abi_len-1]);
for (i=j=0; j<abi_len; j++)
if (abi_well[i].tag!=abi_well[j].tag)
abi_well[++i]=abi_well[j];
abi_len=i+1;
/* construct 'b' sequence tags, and search against 'a' sequence tags */
for (x=i=0; i<abi_size-1; i++, x<<=2)
x|=abi_code(b[i]);
for (count=hit_len=0; i<height; i++, x<<=2) {
x|=abi_code(b[i]);
x&=abi_mask;
for (l=0, r=abi_len-1; l<=r; ) {
m=(l+r)/2;
if (x<abi_well[m].tag)
r=m-1;
else if (x>abi_well[m].tag)
l=m+1;
else {
l=abi_well[m].index-i;
for (j=0; j<hit_len; j++)
if (hit_well[j].diff==l) {
hit_well[j].count++;
if (hit_well[j].count>count) {
count=hit_well[j].count;
diff=hit_well[j].diff;
if (j) {
hit_well[j]=hit_well[0];
hit_well[0].count=count;
hit_well[0].diff=diff;
}
}
break;
}
if (j>=hit_len) {
hit_well[j].count=1;
hit_well[j].diff=l;
hit_len=j+1;
}
break;
}
}
}
/* calculate starting points for sequence a and b */
if (count<=0) {
*start=*end=0;
return;
} else if (diff>=0) {
i=diff; j=0;
} else {
i=0; j=-diff;
}
/* find the primary alignment region first */
for (span=0, left=x=i; i<width && j<height; i++, j++)
if (badness[a[i]][b[j]]) {
/*
for (count=0, m=0, l=i+1, r=j+1;
l<width && r<height && count<VERYBAD && count>condition[m];
m++, l++, r++)
if (badness[a[l]][b[r]]) count+=badness[a[l]][b[r]];
if (l<width && r<height && count<VERYBAD)
continue;
*/
if (i-x>span) {
left=x;
span=i-x;
}
x=i+1;
}
if (i-x>span) {
left=x;
span=i-x;
}
if (span<=0) {
*start=*end=0;
return;
}
/* extend alignment region toward the right, if possible */
for (i=left+span, j=i-diff; i<width && j<height; i++, j++)
if (badness[a[i]][b[j]]) {
x=0;
stack[x].i=i+1; stack[x].j=j+1; stack[x].m=0; stack[x++].c=0;
while (x>0) {
for (count=stack[--x].c, m=stack[x].m, l=stack[x].i, r=stack[x].j;
l<width && r<height && badness[a[l]][b[r]]==0
&& count>condition[m];
m++, l++, r++) ;
if (l>=width || r>=height)
continue;
if (count<=condition[m])
break;
if ((count+=badness[a[l]][b[r]])<VERYBAD) {
stack[x].i=l; stack[x].j=r+1; stack[x].m=m; stack[x++].c=count;
stack[x].i=l+1; stack[x].j=r; stack[x].m=m+1; stack[x++].c=count;
stack[x].i=l+1; stack[x].j=r+1; stack[x].m=m+1; stack[x++].c=count;
}
}
if (l<width && r<height && count<=condition[m])
continue;
x=0;
stack[x].i=i+1; stack[x].j=j; stack[x].m=0; stack[x++].c=0;
while (x>0) {
for (count=stack[--x].c, m=stack[x].m, l=stack[x].i, r=stack[x].j;
l<width && r<height && badness[a[l]][b[r]]==0
&& count>condition[m];
m++, l++, r++) ;
if (l>=width || r>=height)
continue;
if (count<=condition[m])
break;
if ((count+=badness[a[l]][b[r]])<VERYBAD) {
stack[x].i=l; stack[x].j=r+1; stack[x].m=m; stack[x++].c=count;
stack[x].i=l+1; stack[x].j=r; stack[x].m=m+1; stack[x++].c=count;
stack[x].i=l+1; stack[x].j=r+1; stack[x].m=m+1; stack[x++].c=count;
}
}
if (l<width && r<height && count<=condition[m]) {
j--;
continue;
}
x=0;
stack[x].i=i; stack[x].j=j+1; stack[x].m=0; stack[x++].c=0;
while (x>0) {
for (count=stack[--x].c, m=stack[x].m, l=stack[x].i, r=stack[x].j;
l<width && r<height && badness[a[l]][b[r]]==0
&& count>condition[m];
m++, l++, r++) ;
if (l>=width || r>=height)
continue;
if (count<=condition[m])
break;
if ((count+=badness[a[l]][b[r]])<VERYBAD) {
stack[x].i=l; stack[x].j=r+1; stack[x].m=m; stack[x++].c=count;
stack[x].i=l+1; stack[x].j=r; stack[x].m=m+1; stack[x++].c=count;
stack[x].i=l+1; stack[x].j=r+1; stack[x].m=m+1; stack[x++].c=count;
}
}
if (l<width && r<height && count<=condition[m]) {
i--;
continue;
}
break;
}
span=i-left;
/* extend toward the left, if possible */
for (i=left-1, j=i-diff; i>=0 && j>=0; i--, j--)
if (badness[a[i]][b[j]]) {
x=0;
stack[x].i=i-1; stack[x].j=j-1; stack[x].m=0; stack[x++].c=0;
while (x>0) {
for (count=stack[--x].c, m=stack[x].m, l=stack[x].i, r=stack[x].j;
l>=0 && r>=0 && badness[a[l]][b[r]]==0
&& count>condition[m];
m++, l--, r--) ;
if (l<0 || r<0)
continue;
if (count<=condition[m])
break;
if ((count+=badness[a[l]][b[r]])<VERYBAD) {
stack[x].i=l; stack[x].j=r-1; stack[x].m=m; stack[x++].c=count;
stack[x].i=l-1; stack[x].j=r; stack[x].m=m+1; stack[x++].c=count;
stack[x].i=l-1; stack[x].j=r-1; stack[x].m=m+1; stack[x++].c=count;
}
}
if (l>=0 && r>=0 && count<=condition[m])
continue;
x=0;
stack[x].i=i-1; stack[x].j=j; stack[x].m=0; stack[x++].c=0;
while (x>0) {
for (count=stack[--x].c, m=stack[x].m, l=stack[x].i, r=stack[x].j;
l>=0 && r>=0 && badness[a[l]][b[r]]==0
&& count>condition[m];
m++, l--, r--) ;
if (l<0 || r<0)
continue;
if (count<=condition[m])
break;
if ((count+=badness[a[l]][b[r]])<VERYBAD) {
stack[x].i=l; stack[x].j=r-1; stack[x].m=m; stack[x++].c=count;
stack[x].i=l-1; stack[x].j=r; stack[x].m=m+1; stack[x++].c=count;
stack[x].i=l-1; stack[x].j=r-1; stack[x].m=m+1; stack[x++].c=count;
}
}
if (l>=0 && r>=0 && count<=condition[m]) {
j++;
continue;
}
x=0;
stack[x].i=i; stack[x].j=j-1; stack[x].m=0; stack[x++].c=0;
while (x>0) {
for (count=stack[--x].c, m=stack[x].m, l=stack[x].i, r=stack[x].j;
l>=0 && r>=0 && badness[a[l]][b[r]]==0
&& count>condition[m];
m++, l--, r--) ;
if (l<0 || r<0)
continue;
if (count<=condition[m])
break;
if ((count+=badness[a[l]][b[r]])<VERYBAD) {
stack[x].i=l; stack[x].j=r-1; stack[x].m=m; stack[x++].c=count;
stack[x].i=l-1; stack[x].j=r; stack[x].m=m+1; stack[x++].c=count;
stack[x].i=l-1; stack[x].j=r-1; stack[x].m=m+1; stack[x++].c=count;
}
}
if (l>=0 && r>=0 && count<=condition[m]) {
i++;
continue;
}
break;
}
span=left+span-i-1;
left=i+1;
*start=left;
*end=left+span-1;
}
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