void doinit()
{
/* initializes variables */
inputnumbers2(&spp, &nonodes2, 1);
if (inputnumbers2error)
return;
nonodes2--;
alloctree(&curtree.nodep, nonodes2);
allocd(nonodes2, curtree.nodep);
allocw(nonodes2, curtree.nodep);
alloctree(&bestree.nodep, nonodes2);
allocd(nonodes2, bestree.nodep);
allocw(nonodes2, bestree.nodep);
alloctree(&priortree.nodep, nonodes2);
allocd(nonodes2, priortree.nodep);
allocw(nonodes2, priortree.nodep);
if (njumble > 1) {
alloctree(&bestree2.nodep, nonodes2);
allocd(nonodes2, bestree2.nodep);
allocw(nonodes2, bestree2.nodep);
}
allocrest();
} /* doinit */
void doinit()
{
/* initializes variables */
inputnumbers2(&spp, &nonodes2, 1);
getoptions();
if ( !usertree )
nonodes2--;
alloctree(&curtree.nodep, nonodes2);
allocd(nonodes2, curtree.nodep);
allocw(nonodes2, curtree.nodep);
if (!usertree) {
alloctree(&bestree.nodep, nonodes2);
allocd(nonodes2, bestree.nodep);
allocw(nonodes2, bestree.nodep);
alloctree(&priortree.nodep, nonodes2);
allocd(nonodes2, priortree.nodep);
allocw(nonodes2, priortree.nodep);
if (njumble > 1) {
alloctree(&bestree2.nodep, nonodes2);
allocd(nonodes2, bestree2.nodep);
allocw(nonodes2, bestree2.nodep);
}
}
allocrest();
} /* doinit */
void globrearrange(long* numtrees,boolean* succeeded)
{
/* does global rearrangements */
tree globtree;
tree oldtree;
int i,j,k,num_sibs,num_sibs2;
node *where,*sib_ptr,*sib_ptr2;
double oldbestyet = curtree.likelihood;
int success = false;
alloctree(&globtree.nodep,nonodes2);
alloctree(&oldtree.nodep,nonodes2);
setuptree(&globtree,nonodes2);
setuptree(&oldtree,nonodes2);
allocd(nonodes2, globtree.nodep);
allocd(nonodes2, oldtree.nodep);
allocw(nonodes2, globtree.nodep);
allocw(nonodes2, oldtree.nodep);
copy_(&curtree,&globtree);
copy_(&curtree,&oldtree);
for ( i = spp ; i < nonodes2 ; i++ ) {
num_sibs = count_sibs(curtree.nodep[i]);
if(openloop)return;
sib_ptr = curtree.nodep[i];
if ( (i - spp) % (( nonodes2 / 72 ) + 1 ) == 0 )
putchar('.');
fflush(stdout);
for ( j = 0 ; j <= num_sibs ; j++ ) {
re_move(&sib_ptr,&where);
copy_(&curtree,&priortree);
if (where->tip) {
copy_(&oldtree,&curtree);
copy_(&oldtree,&bestree);
sib_ptr=sib_ptr->next;
continue;
}
else
{
num_sibs2 = count_sibs(where);
if(openloop)return;
}
sib_ptr2 = where;
for ( k = 0 ; k < num_sibs2 ; k++ ) {
addwhere = NULL;
addtraverse(sib_ptr,sib_ptr2->back,true,numtrees,succeeded);
if ( addwhere && where != addwhere && where->back != addwhere
&& bestree.likelihood > globtree.likelihood) {
copy_(&bestree,&globtree);
success = true;
}
sib_ptr2 = sib_ptr2->next;
}
copy_(&oldtree,&curtree);
copy_(&oldtree,&bestree);
sib_ptr = sib_ptr->next;
}
}
copy_(&globtree,&curtree);
copy_(&globtree,&bestree);
if (success && globtree.likelihood > oldbestyet) {
*succeeded = true;
}
else {
*succeeded = false;
}
freed(nonodes2, globtree.nodep);
freed(nonodes2, oldtree.nodep);
freew(nonodes2, globtree.nodep);
freew(nonodes2, oldtree.nodep);
freetree(&globtree.nodep,nonodes2);
freetree(&oldtree.nodep,nonodes2);
}
