LONGMATRIX *new_longmatrix( long nrh, long nch)
{
LONGMATRIX *m;
m=(LONGMATRIX *)malloc(sizeof(LONGMATRIX));
if (!m) t_error("allocation failure in LONGMATRIX()");
m->isdynamic=isDynamic;
m->nrl=NL;
m->nrh=nrh;
m->ncl=NL;
m->nch=nch;
m->co=lmatrix(1,nrh,1,nch);
return m;
}
void head_to_tail(long j, long *npair_per_helix, long **bs_1, long **bs_2,
long *nregions,long **sub_helix1,long **sub_helix2)
/* Account only the real anti-parrellel helix from the longer helix.*/
{
long i, n, m, k, nh, **helix, nregion;
n = npair_per_helix[j];
helix = lmatrix(1, n , 1, 2);
nh=1;
nregion = 1;
for(i=1; i<=n; i++){ /* get the anti-parrellel helix region */
helix[nregion][1] = i;
for(i++;(i<=n)&&
((bs_1[j][i] == bs_1[j][i-1]+1)
&&(bs_2[j][i] == bs_2[j][i-1]-1))
||((bs_2[j][i] == bs_2[j][i-1]+1)
&&(bs_1[j][i] == bs_1[j][i-1]-1))
; i++){
helix[nregion][2] = i;
}
i--;
if(helix[nregion][2] - helix[nregion][1] >= 1){ /* minimum two pairs */
nregion++;
}
}
/* NOTE: each nregions[j] is the real anti-parrallel helix in the longer
helix determined by geometry.
*/
nregions[j] = nregion -1;
for(m=1; m<=nregions[j]; m++){
sub_helix1[j][m] = nh;
for(k = helix[m][1]; k<=helix[m][2]; k++){
bs_1[j][nh]=bs_1[j][k];
bs_2[j][nh]=bs_2[j][k];
nh++;
}
sub_helix2[j][m] = nh-1;
}
npair_per_helix[j]=nh-1;
free_lmatrix(helix, 1, n, 1, 2);
}
