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util19l.c
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/* fprintfCopyrite 1995 Ward Wheeler, all rights reserved*/
/*functions to do alignments the new faster way ala Goloboff*/
#include "align3.h"
alignment **do_swap_thang_align(a,ntax,nodes,l_in,best_aligns,values,a_up,anc,mult,score_holder,parallel_modify)
alignment **a, **best_aligns,***a_up;
int ntax, *l_in, **nodes,parallel_modify;
parameters *values;
int *anc,mult,score_holder;
{
int i,j,k,l,m,kk,num_clipped,check,tot_best,best,d1,d2;
int l_clip, l_rest,cur_best,found_better,node_removed;
int **cur_nodes, *blocked, *is_it_or_desc;
int **hold_nodes,**temp_nodes;
int clipped_base,***reroot_array,cur_num_trees;
int old_length, tree_counter;
int ***best_nodes_new,***best_nodes_old,num_found;
int new_start,all_others;
int where_it_was_anc,where_it_was_desc;
int **temp_nodes_h,whole_length;
int initial_length,d3,d4;
alignment *thing_to_add,*temp_align,*temp_align2;
int where_it_was_branch,paren_count;
int is_unique,sent,received;
int ii,jj,this_tree_counter,this_best;
int bytes,info,bufid,source,type;
int will_be_OK,**cur_groups,ngroups2;
int num_best, ***corres,all_rest;
alignment **best_aligns_holder,**a_down;
alignment **a_down_buf, **a_buf, ***a_up_buf;
int ***corres_buf,x,y,up_node,down_node;
alignment *up_temp, **check_buf;
int int_holder,in_trees,g_test;
char *collapse_name;
up_temp=NULL;
check_buf=NULL;
collapse_name=NULL;
values->support=NULL;
/*allocations*/
if (values->new_optimization) {
a_down=(alignment **)malloc((2*ntax-1)*sizeof(alignment *));
assert((int) a_down);
for (i=0;i<2*ntax-1;i++) a_down[i]=NULL;
corres=(int ***)malloc((2*(ntax))*sizeof(int **));
assert((int) corres);
for (i=0;i<2*ntax;i++) corres[i]=NULL;
for (i=0;i<ntax-1;i++) a_down[i]=make_align(a[i]);
corres_buf=(int ***)malloc((2*(ntax))*sizeof(int **));
assert((int) corres_buf);
for (i=0;i<2*ntax;i++) corres_buf[i]=NULL;
check_buf=(alignment **)malloc((2*ntax-1)*sizeof(alignment *));
assert((int) check_buf);
for (i=0;i<2*ntax-1;i++) check_buf[i]=NULL;
for (i=0;i<ntax-1;i++) check_buf[i]=make_align(a[i]);
if (mult && (values->collapse != 2)) {
collapse_name=(char *)malloc(MAX_SEQUENCE_SIZE*sizeof(char ));
assert((int) collapse_name);
values->support=(int **)malloc(values->keep_aligns*sizeof(int *));
assert((int) values->support);
for (i=0;i<values->keep_aligns;i++) {
values->support[i]=(int *)malloc(ntax*sizeof(int));
assert((int) values->support[i]);
for (j=0;j<ntax;j++) values->support[0][j]=0;
}
}
}
a_down_buf=(alignment **)malloc((2*ntax-1)*sizeof(alignment *));
assert((int) a_down_buf);
for (i=0;i<2*ntax-1;i++) a_down_buf[i]=NULL;
for (i=0;i<ntax-1;i++) a_down_buf[i]=make_align(a[i]);
if (values->tbr_align_shortcut) {
a_buf=(alignment **)malloc((2*ntax-1)*sizeof(alignment *));
assert((int) a_buf);
for (i=0;i<2*ntax-1;i++) a_buf[i]=NULL;
for (i=0;i<ntax-1;i++) a_buf[i]=make_align(a[i]);
a_up_buf=(alignment ***)malloc(((2*ntax)-1)*sizeof(alignment **));
assert((int) a_up_buf);
for (i=0;i<2*ntax-1;i++) {
a_up_buf[i]=(alignment **)malloc(2*sizeof(alignment *));
assert((int) a_up_buf[i]);
a_up_buf[i][0]=NULL;
a_up_buf[i][1]=NULL;
}
}
temp_nodes_h=(int **)malloc((ntax-1)*sizeof(int *));
assert((int)temp_nodes_h);
for (j=0;j<ntax-1;j++) {
temp_nodes_h[j]=(int *)malloc(2*sizeof(int));
assert((int)temp_nodes_h);
}
best_nodes_new=(int ***)malloc(values->keep_aligns*sizeof(int **));
assert((int) best_nodes_new);
best_nodes_old=(int ***)malloc(values->keep_aligns*sizeof(int **));
assert((int) best_nodes_old);
for (i=0;i<values->keep_aligns;i++) {
best_nodes_new[i]=(int **)malloc((ntax-1)*sizeof(int *));
assert((int) best_nodes_new[i]);
best_nodes_old[i]=(int **)malloc((ntax-1)*sizeof(int *));
assert((int) best_nodes_old[i]);
for (j=0;j<ntax-1;j++) {
best_nodes_new[i][j]=(int *)malloc(2*sizeof(int));
assert((int) best_nodes_new[i][j]);
best_nodes_old[i][j]=(int *)malloc(2*sizeof(int));
assert((int) best_nodes_old[i][j]);
}
}
hold_nodes=(int **)malloc((ntax-1)*sizeof(int *));
assert((int) hold_nodes);
cur_nodes=(int **)malloc((ntax-1)*sizeof(int *));
assert((int) cur_nodes);
temp_nodes=(int **)malloc((ntax-1)*sizeof(int *));
assert((int) temp_nodes);
for (k=0;k<ntax-1;k++) {
cur_nodes[k]=(int *)malloc(2*sizeof(int));
assert((int) cur_nodes[k]);
hold_nodes[k]=(int *)malloc(2*sizeof(int));
assert((int) hold_nodes[k]);
temp_nodes[k]=(int *)malloc(2*sizeof(int));
assert((int) temp_nodes[k]);
}
blocked=(int *)malloc((2*(ntax-1))*sizeof(int));
assert((int) blocked);
is_it_or_desc=(int *)malloc(((2*ntax)-1)*sizeof(int));
assert((int) is_it_or_desc);
if ((values->atbr) || (values->arrt)) {
reroot_array=(int ***)malloc((2*ntax-3)*sizeof(int **));
assert((int) reroot_array);
for (i=0;i<2*ntax-3;i++) {
reroot_array[i]=(int **)malloc((ntax-1)*sizeof(int *));
assert((int) reroot_array[i]);
for (j=0;j<ntax-1;j++) {
reroot_array[i][j]=(int *)malloc(2*sizeof(int));
assert((int) reroot_array[i][j]);
}
}
}
will_be_OK=1;
if (!mult) if (!(PARALLEL && values->jackboot)) fprintf(stderr,"Initial build yielded an alignment at length %d\n",best_aligns[0]->score);
paren_count=0;
thing_to_add=NULL;
temp_align=NULL;
temp_align2=NULL;
for (k=0;k<ntax-1;k++) {
best_nodes_new[0][k][0]=best_nodes_old[0][k][0]=nodes[k][0];
best_nodes_new[0][k][1]=best_nodes_old[0][k][1]=nodes[k][1];
}
new_start=num_found=0;
tot_best=old_length=initial_length=best_aligns[0]->score;
cur_num_trees=1;
found_better=1;
tree_counter=(*l_in);/*shoulf always be 1*/
while (found_better) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr,"(swapping");
found_better=0;
old_length=tot_best;
for (m=new_start;m<cur_num_trees;m++) {
/*if (!(PARALLEL*parallel_modify)) fprintf(stderr,"S on %d (%d->%d) ",m,new_start,cur_num_trees);*/
/*copy nodes*/
for (k=0;k<ntax-1;k++) {
hold_nodes[k][0]=best_nodes_old[m][k][0];
hold_nodes[k][1]=best_nodes_old[m][k][1];
anc[hold_nodes[k][0]]=anc[hold_nodes[k][1]]=k+ntax;
}
anc[ntax]=ntax;
/*initialize buffer with down passes should be parallel if can*/
if (values->new_optimization) {
if (!(PARALLEL*parallel_modify)) {
check=all_diagnose_tree_here(a_down_buf,hold_nodes,ntax,ntax,values,HUGE_COST);
if (values->tbr_align_shortcut) get_up_pass_new_opt(a_buf,a_down_buf,a_up_buf,hold_nodes,ntax,values,ntax,anc);
}
else {
check=all_diagnose_tree_here_parallel(a_down_buf,hold_nodes,ntax,ntax,values,0,corres_buf);
if (values->tbr_align_shortcut) get_up_pass_new_opt_parallel(a_buf,a_down_buf,a_up_buf,hold_nodes,ntax,values,ntax,anc);
}
if (mult && (values->collapse!=2)) {
g_test=0;
for (k=0;k<ntax;k++) g_test+=values->support[0][k];
/*collapse and get groups*/
if (!g_test) check=get_collapsed_thang_with_groups_old(best_aligns[0],hold_nodes,ntax,check_buf,PARALLEL*parallel_modify*1,values,values->support[0]);
}
}
else {
if (!(PARALLEL*parallel_modify)) check=all_diagnose_tree_local2(a_down_buf,hold_nodes,ntax,ntax,values);/*get down passes*/
else check=all_diagnose_tree_local_parallel2(a_down_buf,hold_nodes,ntax,ntax,values);
}
sent=received=0;
for (i=2;i<2*(ntax-1);i++) {
/*if (!(PARALLEL*parallel_modify)) fprintf(stderr,"i%d ",i);*/
/*copy nodes*/
for (k=0;k<ntax-1;k++) {
cur_nodes[k][0]=hold_nodes[k][0];
cur_nodes[k][1]=hold_nodes[k][1];
anc[hold_nodes[k][0]]=anc[hold_nodes[k][1]]=k+ntax;
}
anc[ntax]=ntax;
/*choose*/
d1=i/2;
d2=i%2;
/*get size*/
num_clipped=get_size(ntax,cur_nodes,d1,d2,blocked,i,is_it_or_desc,anc);
if (!values->atbr) values->number+=((2*(ntax-num_clipped))-3);
else {
if (num_clipped>1) values->number+=(((2*num_clipped)-3)*((2*(ntax-num_clipped))-3));
else values->number+=((2*(ntax-num_clipped))-3);
}
if (num_clipped<=(ntax-3)) {
/*redo nodes*/
node_removed=anc[cur_nodes[d1][d2]];
where_it_was_anc=anc[node_removed];
if (cur_nodes[anc[node_removed]-ntax][0]==node_removed) {
cur_nodes[anc[node_removed]-ntax][0]=cur_nodes[d1][!d2];
blocked[2*(anc[node_removed]-ntax)]=1;
where_it_was_desc=cur_nodes[anc[node_removed]-ntax][0];
where_it_was_branch=0;
}
else {
cur_nodes[anc[node_removed]-ntax][1]=cur_nodes[d1][!d2];
blocked[2*(anc[node_removed]-ntax)+1]=1;
where_it_was_desc=cur_nodes[anc[node_removed]-ntax][1];
where_it_was_branch=1;
}
anc[cur_nodes[d1][!d2]]=anc[node_removed];
cur_nodes[d1][!d2]=cur_nodes[d1][d2];
anc[node_removed]=node_removed;
if (PARALLEL*parallel_modify) {
if (sent < (values->num_hosts-1)) {
pvm_initsend( PvmDataDefault );
/*pack stuff*/
pvm_pkint(&num_clipped,1,1);
for (ii=0;ii<ntax-1;ii++) pvm_pkint(cur_nodes[ii],2,1);
pvm_pkint(anc,((2*ntax)-1),1);
pvm_pkint(&d1,1,1);
pvm_pkint(&d2,1,1);
pvm_pkint(&where_it_was_desc,1,1);
pvm_pkint(&where_it_was_anc,1,1);
pvm_pkint(&where_it_was_branch,1,1);
pvm_pkint(&score_holder,1,1);
pvm_pkint(&old_length,1,1);
pvm_pkint(blocked,(2*(ntax-1)),1);
pvm_pkint(&node_removed,1,1);
pvm_pkint(&mult,1,1);
pvm_pkint(is_it_or_desc,((2*ntax)-1),1);
for (ii=ntax+1;ii<2*ntax-1;ii++) pack_align(a_down_buf[ii]);
if (values->tbr_align_shortcut) for (ii=ntax+1;ii<2*ntax-1;ii++) pack_align(a_buf[ii]);
pvm_send(values->tids[++sent],PVM_NEW_SWAP);
/*if (!(PARALLEL*parallel_modify)) fprintf(stderr,"S->%d ",sent);*/
}
else {
bufid=pvm_recv(-1,PVM_NEW_SWAP_DONE);
if (bufid) {
info=pvm_bufinfo(bufid, &bytes, &type, &source);
/*unpack stuff*/
pvm_upkint(&this_best,1,1); /*pack cost*/
if ((this_best<tot_best) || ((this_best==tot_best) && mult && (tree_counter< values->keep_aligns))) {
pvm_upkint(&this_tree_counter,1,1);/*pack #solns*/
if (!mult) {
if (this_best<tot_best) this_tree_counter=1;
else this_tree_counter=0;
}
if (this_best<tot_best) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr," Found better at %d\n",this_best);
found_better=1;
tot_best=this_best;
/*unpack the first and then treat the rest like additional solutions*/
for (ii=0;ii<tree_counter;ii++) if (best_aligns[ii]) best_aligns[ii]=dump_align(best_aligns[ii]);
for (jj=0;jj<ntax-1;jj++) pvm_upkint(best_nodes_new[0][jj],2,1);
best_aligns[0]=unpack_align_and_score(values);
if (values->new_optimization && (values->collapse!=2)){
if (!mult) check=get_collapsed_thang(best_aligns[0],best_nodes_new[0],ntax,check_buf,PARALLEL*parallel_modify*0,values);
else check=get_collapsed_thang_with_groups_old(best_aligns[0],best_nodes_new[0],ntax,check_buf,PARALLEL*parallel_modify*0,values,values->support[0]);
best_aligns[0]->score=tot_best;
}
tree_counter=1;
/*rest 1->this_tree_counter*/
for (ii=1;ii<this_tree_counter;ii++) { /*make sure OK when no solutions found*/
for (jj=0;jj<ntax-1;jj++) pvm_upkint(temp_nodes_h[jj],2,1);
if (temp_align) temp_align=dump_align(temp_align);
temp_align=unpack_align_and_score(values);
is_unique=1;
if (tree_counter < values->keep_aligns) {
if (!values->new_optimization) for (k=0;k<tree_counter;k++) is_unique*=compare_aligns(temp_align,best_aligns[k]);
else {
if (values->collapse==2) is_unique=is_unique_tree(temp_nodes_h,best_nodes_new,tree_counter,best_nodes_old,cur_num_trees,old_length+1,tot_best,ntax);
else is_unique=is_unique_tree_align(best_aligns,temp_nodes_h,best_nodes_new,tree_counter,best_nodes_old,cur_num_trees,old_length+1,tot_best,ntax,check_buf,PARALLEL*parallel_modify*0,values,collapse_name);
}
if (is_unique) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr," Found another for %d\n",tree_counter+1);
found_better=1;
best_aligns[tree_counter]=make_align(temp_align);
for (k=0;k<ntax-1;k++) {
best_nodes_new[tree_counter][k][0]=temp_nodes_h[k][0];
best_nodes_new[tree_counter][k][1]=temp_nodes_h[k][1];
}
if (values->new_optimization && (values->collapse!=2)) {
free(best_aligns[tree_counter]->name);
best_aligns[tree_counter]->name=(char *)malloc((1+strlen(collapse_name))*sizeof(char));
assert((int) best_aligns[tree_counter]->name);
best_aligns[tree_counter]->name=(char *)strcpy(best_aligns[tree_counter]->name,collapse_name);
}
++tree_counter;
}
}
}
}
else {
for (ii=0;ii<this_tree_counter;ii++) { /*make sure OK when no solutions found*/
for (jj=0;jj<ntax-1;jj++) pvm_upkint(temp_nodes_h[jj],2,1);
if (temp_align) temp_align=dump_align(temp_align);
temp_align=unpack_align_and_score(values);
is_unique=1;
if (tree_counter < values->keep_aligns) {
if (!values->new_optimization) for (k=0;k<tree_counter;k++) is_unique*=compare_aligns(temp_align,best_aligns[k]);
else {
if (values->collapse==2) is_unique=is_unique_tree(temp_nodes_h,best_nodes_new,tree_counter,best_nodes_old,cur_num_trees,old_length+1,tot_best,ntax);
else is_unique=is_unique_tree_align(best_aligns,temp_nodes_h,best_nodes_new,tree_counter,best_nodes_old,cur_num_trees,old_length+1,tot_best,ntax,check_buf,PARALLEL*parallel_modify*0,values,collapse_name);
}
if (is_unique) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr," Found another for %d\n",tree_counter+1);
found_better=1;
best_aligns[tree_counter]=make_align(temp_align);
for (k=0;k<ntax-1;k++) {
best_nodes_new[tree_counter][k][0]=temp_nodes_h[k][0];
best_nodes_new[tree_counter][k][1]=temp_nodes_h[k][1];
}
if (values->new_optimization && (values->collapse!=2)) {
free(best_aligns[tree_counter]->name);
best_aligns[tree_counter]->name=(char *)malloc((1+strlen(collapse_name))*sizeof(char));
assert((int) best_aligns[tree_counter]->name);
best_aligns[tree_counter]->name=(char *)strcpy(best_aligns[tree_counter]->name,collapse_name);
}
++tree_counter;
}
}
}
}/*else equal*/
}
++received;
}
pvm_initsend( PvmDataDefault );
/*pack stuff*/
pvm_pkint(&num_clipped,1,1);
for (ii=0;ii<ntax-1;ii++) pvm_pkint(cur_nodes[ii],2,1);
pvm_pkint(anc,((2*ntax)-1),1);
pvm_pkint(&d1,1,1);
pvm_pkint(&d2,1,1);
pvm_pkint(&where_it_was_desc,1,1);
pvm_pkint(&where_it_was_anc,1,1);
pvm_pkint(&where_it_was_branch,1,1);
pvm_pkint(&score_holder,1,1);
pvm_pkint(&old_length,1,1);
pvm_pkint(blocked,(2*(ntax-1)),1);
pvm_pkint(&node_removed,1,1);
pvm_pkint(&mult,1,1);
pvm_pkint(is_it_or_desc,((2*ntax)-1),1);
for (ii=ntax+1;ii<2*ntax-1;ii++) pack_align(a_down_buf[ii]);
if (values->tbr_align_shortcut) for (ii=ntax+1;ii<2*ntax-1;ii++) pack_align(a_buf[ii]);
pvm_send(source,PVM_NEW_SWAP);
++sent;
}
}
else {
/*when one or two taxa*/
if ((num_clipped < 3) || (!values->atbr)) { /*if no alternative roots or sbr*/
if (!values->new_optimization) {
check=all_diagnose_tree_local2(a,cur_nodes,ntax,ntax,values);
/*check=all_diagnose_tree_local3(a,cur_nodes,ntax,ntax,values,is_it_or_desc);
for (k=ntax+1;k<2*ntax-1;k++) if (is_it_or_desc[k]) {
if (a[k]) a[k]=dump_align(a[k]);
a[k]=make_align(a_down_buf[k]);
}*/
get_up_pass2(a,cur_nodes,ntax,values,a_up,ntax,anc);
}
else {
check=all_diagnose_tree_local_new_opt2(a_down,cur_nodes,ntax,ntax,values,node_removed,corres,is_it_or_desc);
/*get up_pass alignments*/
get_up_pass_new_opt2(a,a_down,a_up,cur_nodes,ntax,values,ntax,anc,corres,node_removed,is_it_or_desc);
}
/* get "best" set sequences[cur_nodes[d1][d2]] as XUY */
d3=cur_nodes[d1][d2];
if (d3<ntax) d3-=1;
d4=where_it_was_desc;
if (d4<ntax) d4-=1;
if (thing_to_add) thing_to_add=dump_align(thing_to_add);
thing_to_add=make_align(a_down_buf[d3]);
if (!values->new_optimization) {
if (temp_align) temp_align=dump_align(temp_align);
if (where_it_was_anc>ntax) temp_align=nw(a_up[where_it_was_anc][where_it_was_branch],a[d4],values);
else temp_align=make_align(a[d4]);
if (score_holder>0) {
values->phylo_score=score_holder;
temp_align->score=cladogram(temp_align,values);
values->phylo_score=0;
}
/*redo score with phyloshit*/
best=old_length-temp_align->score;
}
else {
all_rest=thing_to_add->score + a_down[cur_nodes[0][1]]->score;
best=old_length - all_rest;
/*values->in_optimize=1;
temp_align2=nw(a[where_it_was_anc],a[d4],values);
values->in_optimize=0;
temp_align2=newer_make_ambig(temp_align2,values);
temp_align=nw(temp_align2,thing_to_add,values);
if (!(PARALLEL*parallel_modify)) fprintf(stderr,"{OB %d NB ",best);
best=temp_align2->score;
if (!(PARALLEL*parallel_modify)) fprintf(stderr,"%d}",best);
all_rest=old_length-best;
if (temp_align) temp_align=dump_align(temp_align);
if (temp_align2) temp_align2=dump_align(temp_align2);*/
/*values->in_optimize=1;
temp_align=nw(a[where_it_was_anc],a[cur_nodes[where_it_was_anc - ntax][where_it_was_branch]],values);
values->in_optimize=0;
temp_align=newer_make_ambig(temp_align,values);
temp_align2=nw(thing_to_add,temp_align,values);
if (!(PARALLEL*parallel_modify)) fprintf(stderr,"OB %d NB ",best);
best=temp_align2->score;
if (!(PARALLEL*parallel_modify)) fprintf(stderr,"%d ",best);
all_rest=old_length-best;
if (!(PARALLEL*parallel_modify)) fprintf(stderr,"{%d %d %d %d}",best,thing_to_add->score,a_down[cur_nodes[0][1]]->score,old_length);
if (temp_align) temp_align=dump_align(temp_align);
if (temp_align2) temp_align2=dump_align(temp_align2);*/
}
if (((best==0) && (mult)) || (best>0)) {/*to make sure that that sequence matters ie adds length*/
/*loop through places to put back*/
blocked[1]=0;
for (j=1;j<(2*(ntax-1));j++) if (!blocked[j]) { /*regraft 'in principle' */
if (values->groups) {
for (ii=0;ii<ntax-1;ii++) for (jj=0;jj<2;jj++) temp_nodes[ii][jj]=cur_nodes[ii][jj];
check=temp_nodes[j/2][j%2];
temp_nodes[j/2][j%2]=node_removed;
temp_nodes[d1][!d2]=check;
cur_groups=get_cur_groups(temp_nodes,ntax,ntax,&ngroups2);
will_be_OK=compare_groups(values->groups,cur_groups,values->ngroups,ngroups2,ntax-1,ntax-1);
for (ii=0;ii<ngroups2;ii++) free(cur_groups[ii]);
free(cur_groups);
}
if (will_be_OK) {
/* get_cost*/
if (temp_align) temp_align=dump_align(temp_align);
if (temp_align2) temp_align2=dump_align(temp_align2);
d3=cur_nodes[j/2][j%2];
if (d3<ntax) d3-=1;
if (!values->new_optimization) {
temp_align=nw(thing_to_add,a[d3],values);
if (j>1) {
/*if (!(PARALLEL*parallel_modify)) fprintf(stderr,"{");*/
d4=(j/2)+ntax;
temp_align2=nw(temp_align,a_up[d4][j%2],values);
if (score_holder>0) {
if (!compare_aligns(temp_align2,values->previous)) temp_align2->score=values->previous->score;
else {
values->phylo_score=score_holder;
temp_align2->score=cladogram(temp_align2,values);
values->phylo_score=0;
if (values->previous) values->previous=dump_align(values->previous);
values->previous=make_align(temp_align2);
}
}
cur_best=temp_align2->score;
/*if (!(PARALLEL*parallel_modify)) fprintf(stderr,"}");*/
}
else {
/*if (!(PARALLEL*parallel_modify)) fprintf(stderr,"(");*/
if (score_holder>0) {
if (!compare_aligns(temp_align,values->previous)) temp_align->score=values->previous->score;
else {
values->phylo_score=score_holder;
temp_align->score=cladogram(temp_align,values);
values->phylo_score=0;
if (values->previous) values->previous=dump_align(values->previous);
values->previous=make_align(temp_align);
}
}
cur_best=temp_align->score;
/*if (!(PARALLEL*parallel_modify)) fprintf(stderr,")");*/
}
}
else {
d4=(j/2)+ntax;
if (j>1) {
values->in_optimize=1;
temp_align2=nw(a[d3],a[d4],values);
values->in_optimize=0;
temp_align2=newer_make_ambig(temp_align2,values);
temp_align=nw(temp_align2,thing_to_add,values);
}
else temp_align=nw(thing_to_add,a_down[cur_nodes[0][1]],values);
cur_best=temp_align->score+all_rest;
}
/*filter for type wieight problem for now*/
if (values->new_optimization) {
/*if (1) {*/
if ((cur_best < tot_best) || ((cur_best == tot_best) && mult && (tree_counter< values->keep_aligns))) {
for (ii=0;ii<ntax-1;ii++) for (jj=0;jj<2;jj++) temp_nodes[ii][jj]=cur_nodes[ii][jj];
check=temp_nodes[j/2][j%2];
temp_nodes[j/2][j%2]=node_removed;
temp_nodes[d1][!d2]=check;
check=cur_best;
cur_best=all_diagnose_tree_local_new_opt(check_buf,temp_nodes,ntax,ntax,values,0,corres);
/*if (cur_best != check) if (!(PARALLEL*parallel_modify)) fprintf(stderr,".(%d %d)",check,cur_best);
else if (!(PARALLEL*parallel_modify)) fprintf(stderr,"+");*/
}
}
if (cur_best < tot_best) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr," Found better at %d\n",cur_best);
tot_best=cur_best;
found_better=1;
for (k=0;k<ntax-1;k++) {
best_nodes_new[0][k][0]=cur_nodes[k][0];
best_nodes_new[0][k][1]=cur_nodes[k][1];
}
check=best_nodes_new[0][j/2][j%2];
best_nodes_new[0][j/2][j%2]=node_removed;
best_nodes_new[0][d1][!d2]=check;
/*add best_aligns stuf free first*/
for (k=0;k<tree_counter;k++) if (best_aligns[k]) best_aligns[k]=dump_align(best_aligns[k]);
if (temp_align2) best_aligns[0]=make_align(temp_align2);
else best_aligns[0]=make_align(temp_align);
if (values->new_optimization && (values->collapse != 2)) {
/*redo name for collapse*/
if (!mult) check=get_collapsed_thang(best_aligns[0],best_nodes_new[0],ntax,check_buf,PARALLEL*parallel_modify*1,values);
else check=get_collapsed_thang_with_groups_old(best_aligns[0],best_nodes_new[0],ntax,check_buf,PARALLEL*parallel_modify*1,values,values->support[0]);
best_aligns[0]->score=tot_best;
}
tree_counter=1;
}
else if ((cur_best == tot_best) && mult && (tree_counter< values->keep_aligns)) {
/*if (!(PARALLEL*parallel_modify)) fprintf(stderr,"F");*/
for (k=0;k<ntax-1;k++) {
best_nodes_new[tree_counter][k][0]=cur_nodes[k][0];
best_nodes_new[tree_counter][k][1]=cur_nodes[k][1];
}
check=best_nodes_new[tree_counter][j/2][j%2];
best_nodes_new[tree_counter][j/2][j%2]=node_removed;
best_nodes_new[tree_counter][d1][!d2]=check;
/*chec to see if novel*/
is_unique=1;
if (!values->new_optimization) {
if (temp_align2) for (k=0;k<tree_counter;k++) is_unique*=compare_aligns(temp_align2,best_aligns[k]);
else for (k=0;k<tree_counter;k++) is_unique*=compare_aligns(temp_align,best_aligns[k]);
}
else {
if (values->collapse==2) is_unique=is_unique_tree(best_nodes_new[tree_counter],best_nodes_new,tree_counter,best_nodes_old,cur_num_trees,old_length,tot_best,ntax);
else is_unique=is_unique_tree_align(best_aligns,best_nodes_new[tree_counter],best_nodes_new,tree_counter,best_nodes_old,cur_num_trees,old_length,tot_best,ntax,check_buf,PARALLEL*parallel_modify*1,values,collapse_name);
}
if (is_unique) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr," Found another for %d\n",tree_counter+1);
found_better=1;
if (temp_align2) best_aligns[tree_counter]=make_align(temp_align2);
else best_aligns[tree_counter]=make_align(temp_align);
if (values->new_optimization && (values->collapse!=2)) {
free(best_aligns[tree_counter]->name);
best_aligns[tree_counter]->name=(char *)malloc((1+strlen(collapse_name))*sizeof(char));
assert((int) best_aligns[tree_counter]->name);
best_aligns[tree_counter]->name=(char *)strcpy(best_aligns[tree_counter]->name,collapse_name);
}
++tree_counter;
}
/*if (!(PARALLEL*parallel_modify)) fprintf(stderr,"O");*/
}
} /*SBR loop--regrafted*/
}/*will it be OK*/
} /*BEST split size ok*/
}/*too few clipped or SBR*/
else { /*TBR with at least three taxa*/
check=get_root_array(reroot_array,num_clipped,node_removed,cur_nodes,d1,d2,ntax,is_it_or_desc,anc);
if (!values->new_optimization) {
/*fix so no do if in group*/
check=all_diagnose_tree_local2(a,cur_nodes,ntax,ntax,values);
/*check=all_diagnose_tree_local3(a,cur_nodes,ntax,ntax,values,is_it_or_desc);
for (k=ntax+1;k<2*ntax-1;k++) if (is_it_or_desc[k]) {
if (a[k]) a[k]=dump_align(a[k]);
a[k]=make_align(a_down_buf[k]);
}*/
get_up_pass2(a,cur_nodes,ntax,values,a_up,ntax,anc);
}
else {
/*only down pass if ! in picked*/
check=all_diagnose_tree_local_new_opt2(a_down,cur_nodes,ntax,ntax,values,node_removed,corres,is_it_or_desc);
/*get up_pass alignments*/
get_up_pass_new_opt2(a,a_down,a_up,cur_nodes,ntax,values,ntax,anc,corres,node_removed,is_it_or_desc);
}
for (l=0;l<2*num_clipped-3;l++) {
/*only down pass if in picked*/
d3=reroot_array[l][d1][d2];
if (d3<ntax) d3-=1;
d4=where_it_was_desc;
if (d4<ntax) d4-=1;
if (thing_to_add) thing_to_add=dump_align(thing_to_add);
/*if same rooting as original use the buffer*/
if ((cur_nodes[cur_nodes[d1][d2]-ntax][0]==reroot_array[l][reroot_array[l][d1][d2]-ntax][0]) &&(cur_nodes[cur_nodes[d1][d2]-ntax][1]==reroot_array[l][reroot_array[l][d1][d2]-ntax][1])) thing_to_add=make_align(a_down_buf[d3]);
else if (values->tbr_align_shortcut) { /*X U Y*/
if (values->new_optimization) {
x=reroot_array[l][reroot_array[l][d1][d2]-ntax][0];
y=reroot_array[l][reroot_array[l][d1][d2]-ntax][1];
if (x<ntax) x-=1;
if (y<ntax) y-=1;
thing_to_add=nw(a_buf[x],a_buf[y],values);
}
else {/*currently disabled*/
/*get X and Y*/
x=reroot_array[l][reroot_array[l][d1][d2]-ntax][0];
y=reroot_array[l][reroot_array[l][d1][d2]-ntax][1];
if (x<ntax) {
down_node=x;
up_node=y;
}
else if (y<ntax) {
down_node=y;
up_node=x;
}
else {
if (cur_nodes[y-ntax][0]==x) { down_node=x; up_node=y;}
else if (cur_nodes[y-ntax][1]==x) { down_node=x; up_node=y; }
else if (cur_nodes[x-ntax][0]==y) { down_node=y; up_node=x; }
else { down_node=y; up_node=x; }
}
/*get the up*/
if (up_temp) up_temp=dump_align(up_temp);
up_temp=get_single_up(a_down_buf[down_node],a_down_buf[cur_nodes[d1][d2]],values);
/*make it*/
if (down_node<ntax) x-=1;
thing_to_add=nw(a_down_buf[down_node],up_temp,values);
if (up_temp) up_temp=dump_align(up_temp);
}
}
else {
if (!values->new_optimization) check=all_diagnose_tree_local3(a,reroot_array[l],ntax,ntax,values,is_it_or_desc); /*,is_it_or_desc); get down passes*/
else check=all_diagnose_tree_local_new_opt3(a_down,reroot_array[l],ntax,ntax,values,node_removed,corres,is_it_or_desc);
if (!values->new_optimization) thing_to_add=make_align(a[d3]);
else thing_to_add=make_align(a_down[d3]);
}
if (!values->new_optimization) {
if (temp_align) temp_align=dump_align(temp_align);
if (where_it_was_anc>ntax) temp_align=nw(a_up[where_it_was_anc][where_it_was_branch],a[d4],values);
else temp_align=make_align(a[d4]);
if (score_holder>0) {
values->phylo_score=score_holder;
temp_align->score=cladogram(temp_align,values);
values->phylo_score=0;
}
/*redo score with phyloshit*/
best=old_length-temp_align->score;
}
else {
all_rest=thing_to_add->score + a_down[reroot_array[l][0][1]]->score;
best=old_length - all_rest;
}
if ((best>0) || ((best==0) && (mult))) {/*to make sure that that sequence matters ie adds length*/
/*loop through places to put back*/
blocked[1]=0;
for (j=1;j<(2*(ntax-1));j++) if (!blocked[j]) { /*regraft 'in principle' */
if (values->groups) {
for (ii=0;ii<ntax-1;ii++) for (jj=0;jj<2;jj++) temp_nodes[ii][jj]=reroot_array[l][ii][jj];
check=temp_nodes[j/2][j%2];
temp_nodes[j/2][j%2]=node_removed;
temp_nodes[d1][!d2]=check;
cur_groups=get_cur_groups(temp_nodes,ntax,ntax,&ngroups2);
will_be_OK=compare_groups(values->groups,cur_groups,values->ngroups,ngroups2,ntax-1,ntax-1);
for (ii=0;ii<ngroups2;ii++) free(cur_groups[ii]);
free(cur_groups);
}
if (will_be_OK) {
/* get_cost*/
if (temp_align) temp_align=dump_align(temp_align);
if (temp_align2) temp_align2=dump_align(temp_align2);
d3=reroot_array[l][j/2][j%2];
if (d3<ntax) d3-=1;
if (!values->new_optimization) {
temp_align=nw(thing_to_add,a[d3],values);
if (j>1) {
/*if (!(PARALLEL*parallel_modify)) fprintf(stderr,"{");*/
d4=(j/2)+ntax;
temp_align2=nw(temp_align,a_up[d4][j%2],values);
if (score_holder>0) {
if (!compare_aligns(temp_align2,values->previous)) temp_align2->score=values->previous->score;
else {
values->phylo_score=score_holder;
temp_align2->score=cladogram(temp_align2,values);
values->phylo_score=0;
if (values->previous) values->previous=dump_align(values->previous);
values->previous=make_align(temp_align2);
}
}
cur_best=temp_align2->score;
/*if (!(PARALLEL*parallel_modify)) fprintf(stderr,"}");*/
}
else {
/*if (!(PARALLEL*parallel_modify)) fprintf(stderr,"(");*/
if (score_holder>0) {
if (!compare_aligns(temp_align,values->previous)) temp_align->score=values->previous->score;
else {
values->phylo_score=score_holder;
temp_align->score=cladogram(temp_align,values);
values->phylo_score=0;
if (values->previous) values->previous=dump_align(values->previous);
values->previous=make_align(temp_align);
}
}
cur_best=temp_align->score;
/*if (!(PARALLEL*parallel_modify)) fprintf(stderr,")");*/
}
}
else {
d4=(j/2)+ntax;
if (j>1) {
values->in_optimize=1;
temp_align2=nw(a[d3],a[d4],values);
values->in_optimize=0;
temp_align2=newer_make_ambig(temp_align2,values);
temp_align=nw(temp_align2,thing_to_add,values);
}
else temp_align=nw(thing_to_add,a_down[reroot_array[l][0][1]],values);
cur_best=temp_align->score+all_rest;
}
if (values->new_optimization) {
if ((cur_best < tot_best) || ((cur_best == tot_best) && mult && (tree_counter< values->keep_aligns))) {
for (ii=0;ii<ntax-1;ii++) for (jj=0;jj<2;jj++) temp_nodes[ii][jj]=reroot_array[l][ii][jj];
check=temp_nodes[j/2][j%2];
temp_nodes[j/2][j%2]=node_removed;
temp_nodes[d1][!d2]=check;
check=cur_best;
cur_best=all_diagnose_tree_local_new_opt(check_buf,temp_nodes,ntax,ntax,values,0,corres);
/*if (cur_best != check) if (!(PARALLEL*parallel_modify)) fprintf(stderr,".");
else if (!(PARALLEL*parallel_modify)) fprintf(stderr,"+");*/
}
}
if (cur_best < tot_best) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr," Found better at %d\n",cur_best);
tot_best=cur_best;
found_better=1;
for (k=0;k<ntax-1;k++) {
best_nodes_new[0][k][0]=reroot_array[l][k][0];
best_nodes_new[0][k][1]=reroot_array[l][k][1];
}
check=best_nodes_new[0][j/2][j%2];
best_nodes_new[0][j/2][j%2]=node_removed;
best_nodes_new[0][d1][!d2]=check;
/*add best_aligns stuf free first*/
for (k=0;k<tree_counter;k++) if (best_aligns[k]) best_aligns[k]=dump_align(best_aligns[k]);
if (temp_align2) best_aligns[0]=make_align(temp_align2);
else best_aligns[0]=make_align(temp_align);
if (values->new_optimization && (values->collapse != 2)) {
/*redo name for collapse*/
if (!mult) check=get_collapsed_thang(best_aligns[0],best_nodes_new[0],ntax,check_buf,PARALLEL*parallel_modify*1,values);
else check=get_collapsed_thang_with_groups_old(best_aligns[0],best_nodes_new[0],ntax,check_buf,PARALLEL*parallel_modify*1,values,values->support[0]);
best_aligns[0]->score=tot_best;
}
tree_counter=1;
}
else if ((cur_best == tot_best) && mult && (tree_counter< values->keep_aligns)) {
for (k=0;k<ntax-1;k++) {
best_nodes_new[tree_counter][k][0]=reroot_array[l][k][0];
best_nodes_new[tree_counter][k][1]=reroot_array[l][k][1];
}
check=best_nodes_new[tree_counter][j/2][j%2];
best_nodes_new[tree_counter][j/2][j%2]=node_removed;
best_nodes_new[tree_counter][d1][!d2]=check;
/*chec to see if novel*/
is_unique=1;
if (!values->new_optimization) {
if (temp_align2) for (k=0;k<tree_counter;k++) is_unique*=compare_aligns(temp_align2,best_aligns[k]);
else for (k=0;k<tree_counter;k++) is_unique*=compare_aligns(temp_align,best_aligns[k]);
}
else {
if (values->collapse==2) is_unique=is_unique_tree(best_nodes_new[tree_counter],best_nodes_new,tree_counter,best_nodes_old,cur_num_trees,old_length,tot_best,ntax);
else is_unique=is_unique_tree_align(best_aligns,best_nodes_new[tree_counter],best_nodes_new,tree_counter,best_nodes_old,cur_num_trees,old_length,tot_best,ntax,check_buf,PARALLEL*parallel_modify*1,values,collapse_name);
}
if (is_unique) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr," Found another for %d\n",tree_counter+1);
found_better=1;
if (temp_align2) best_aligns[tree_counter]=make_align(temp_align2);
else best_aligns[tree_counter]=make_align(temp_align);
if (values->new_optimization && (values->collapse!=2)) {
free(best_aligns[tree_counter]->name);
best_aligns[tree_counter]->name=(char *)malloc((1+strlen(collapse_name))*sizeof(char));
assert((int) best_aligns[tree_counter]->name);
best_aligns[tree_counter]->name=(char *)strcpy(best_aligns[tree_counter]->name,collapse_name);
}
++tree_counter;
}
}
} /*SBR loop--regrafted*/
}
} /*BEST split size ok*/
}
} /*reroot TBR/SBR choice*/
}/*PARALLEL*parallel_modify*/
} /*size of plucked OK*/
} /*i clades to pick*/
if (PARALLEL*parallel_modify) { /*receive the rest after all I's are sent out and some received */
/*if (!(PARALLEL*parallel_modify)) fprintf(stderr,"In cleanup ");*/
while (received<sent) {
bufid=pvm_recv(-1,PVM_NEW_SWAP_DONE);
if (bufid) {
info=pvm_bufinfo(bufid, &bytes, &type, &source);
/*unpack stuff*/
pvm_upkint(&this_best,1,1); /*pack cost*/
if ((this_best<tot_best) || ((this_best==tot_best) && mult && (tree_counter< values->keep_aligns))) {
pvm_upkint(&this_tree_counter,1,1);/*pack #solns*/
if (!mult) {
if (this_best<tot_best) this_tree_counter=1;
else this_tree_counter=0;
}
if (this_best<tot_best) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr," Found better at %d\n",this_best);
found_better=1;
tot_best=this_best;
/*unpack the first and then treat the rest like additional solutions*/
for (ii=0;ii<tree_counter;ii++) if (best_aligns[ii]) best_aligns[ii]=dump_align(best_aligns[ii]);
for (jj=0;jj<ntax-1;jj++) pvm_upkint(best_nodes_new[0][jj],2,1);
best_aligns[0]=unpack_align_and_score(values);
if (values->new_optimization && (values->collapse!=2)){
if (!mult) check=get_collapsed_thang(best_aligns[0],best_nodes_new[0],ntax,check_buf,PARALLEL*parallel_modify*0,values);
else check=get_collapsed_thang_with_groups_old(best_aligns[0],best_nodes_new[0],ntax,check_buf,PARALLEL*parallel_modify*0,values,values->support[0]);
best_aligns[0]->score=tot_best;
}
tree_counter=1;
/*rest 1->this_tree_counter*/
for (ii=1;ii<this_tree_counter;ii++) { /*make sure OK when no solutions found*/
for (jj=0;jj<ntax-1;jj++) pvm_upkint(temp_nodes_h[jj],2,1);
if (temp_align) temp_align=dump_align(temp_align);
temp_align=unpack_align_and_score(values);
is_unique=1;
if (tree_counter < values->keep_aligns) {
if (!values->new_optimization) for (k=0;k<tree_counter;k++) is_unique*=compare_aligns(temp_align,best_aligns[k]);
else {
if (values->collapse==2) is_unique=is_unique_tree(temp_nodes_h,best_nodes_new,tree_counter,best_nodes_old,cur_num_trees,old_length+1,tot_best,ntax);
else is_unique=is_unique_tree_align(best_aligns,temp_nodes_h,best_nodes_new,tree_counter,best_nodes_old,cur_num_trees,old_length+1,tot_best,ntax,check_buf,PARALLEL*parallel_modify*0,values,collapse_name);
}
if (is_unique) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr," Found another for %d\n",tree_counter+1);
found_better=1;
best_aligns[tree_counter]=make_align(temp_align);
for (k=0;k<ntax-1;k++) {
best_nodes_new[tree_counter][k][0]=temp_nodes_h[k][0];
best_nodes_new[tree_counter][k][1]=temp_nodes_h[k][1];
}
if (values->new_optimization && (values->collapse!=2)) {
free(best_aligns[tree_counter]->name);
best_aligns[tree_counter]->name=(char *)malloc((1+strlen(collapse_name))*sizeof(char));
assert((int) best_aligns[tree_counter]->name);
best_aligns[tree_counter]->name=(char *)strcpy(best_aligns[tree_counter]->name,collapse_name);
}
++tree_counter;
}
}
}
}
/*old way of gathering better solutions
if (this_best<tot_best) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr," Found better at %d\n",this_best);
found_better=1;
for (ii=0;ii<tree_counter;ii++) if (best_aligns[ii]) best_aligns[ii]=dump_align(best_aligns[ii]);
tot_best=this_best;
tree_counter=this_tree_counter;
for (ii=0;ii<tree_counter;ii++){
for (jj=0;jj<ntax-1;jj++) pvm_upkint(best_nodes_new[ii][jj],2,1);
best_aligns[ii]=unpack_align_and_score(values);
if (values->new_optimization && (values->collapse!=2)) {
if (!mult) check=get_collapsed_thang(best_aligns[ii],best_nodes_new[ii],ntax,check_buf,PARALLEL*parallel_modify*1,values);
else check=get_collapsed_thang_with_groups_old(best_aligns[ii],best_nodes_new[ii],ntax,check_buf,PARALLEL*parallel_modify*1,values,values->support[0]);
best_aligns[ii]->score=tot_best;
}
}
}*/
else {
for (ii=0;ii<this_tree_counter;ii++) { /*make sure OK when no solutions found*/
for (jj=0;jj<ntax-1;jj++) pvm_upkint(temp_nodes_h[jj],2,1);
if (temp_align) temp_align=dump_align(temp_align);
temp_align=unpack_align_and_score(values);
is_unique=1;
if (!values->new_optimization) for (k=0;k<tree_counter;k++) is_unique*=compare_aligns(temp_align,best_aligns[k]);
else {
if (values->collapse==2) is_unique=is_unique_tree(temp_nodes_h,best_nodes_new,tree_counter,best_nodes_old,cur_num_trees,old_length+1,tot_best,ntax);
else is_unique=is_unique_tree_align(best_aligns,temp_nodes_h,best_nodes_new,tree_counter,best_nodes_old,cur_num_trees,old_length,tot_best,ntax,check_buf,PARALLEL*parallel_modify*1,values,collapse_name);
}
if (is_unique) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr," Found another for %d\n",tree_counter+1);
found_better=1;
best_aligns[tree_counter]=make_align(temp_align);
for (k=0;k<ntax-1;k++) {
best_nodes_new[tree_counter][k][0]=temp_nodes_h[k][0];
best_nodes_new[tree_counter][k][1]=temp_nodes_h[k][1];
}
if (values->new_optimization && (values->collapse!=2)) {
free(best_aligns[tree_counter]->name);
best_aligns[tree_counter]->name=(char *)malloc((1+strlen(collapse_name))*sizeof(char));
assert((int) best_aligns[tree_counter]->name);
best_aligns[tree_counter]->name=(char *)strcpy(best_aligns[tree_counter]->name,collapse_name);
}
++tree_counter;
}/*unique*/
}/*ii*/
}
}/*if worth dealing*/
}/*bufid*/
++received;
}/*while*/
} /*PARALLEL*parallel_modify*/
/*copy after best is found*/
}/*num trees*/
/*copy over new set of best_nodes*/
if (tree_counter>0) {
if (tot_best < old_length) { /*new trees are better*/
num_found=tree_counter;
new_start=0;
old_length=tot_best;
for (k=0;k<tree_counter;k++) {
for (l=0;l<ntax-1;l++) {
best_nodes_old[k][l][0]=best_nodes_new[k][l][0];
best_nodes_old[k][l][1]=best_nodes_new[k][l][1];
}
}
} /*from zero*/
else { /*New trees are same length as old from cur_num_trees*/
num_found=tree_counter;
new_start=cur_num_trees;
for (k=new_start;k<tree_counter;k++) {
for (l=0;l<ntax-1;l++) {
best_nodes_old[k][l][0]=best_nodes_new[k][l][0];
best_nodes_old[k][l][1]=best_nodes_new[k][l][1];
}
}
}
}
/*reset num_trees*/
cur_num_trees=tree_counter;
/*reroot swapping*/
if (values->arrt) {
if ((found_better) || (!mult && (new_start==0))) { /*found new or original*/
in_trees=tree_counter;
for (kk=new_start;kk<in_trees;kk++) {
/*Get rerootings for each NEW or original solutions*/
for (l=1;l<2*ntax-1;l++) is_it_or_desc[l]=1;
is_it_or_desc[ntax]=0;
for (x=0;x<ntax-1;x++) {
anc[best_nodes_old[kk][x][0]]=x+ntax;
anc[best_nodes_old[kk][x][1]]=x+ntax;
}
check=get_root_array(reroot_array,ntax-1,best_nodes_old[kk][0][1],best_nodes_old[kk],0,1,ntax,is_it_or_desc,anc); /*check these for basal reroot*/
/*get complete down pass length*/
values->number+=((2*(ntax-1))-3);
for (l=0;l<(2*(ntax-1))-3;l++) {
if (!values->new_optimization) {
if (!(PARALLEL*parallel_modify)) cur_best=all_diagnose_tree_local2(a_down_buf,reroot_array[l],ntax,ntax,values);
else cur_best=all_diagnose_tree_local_parallel2(a_down_buf,reroot_array[l],ntax,ntax,values);
}
else {
if (!(PARALLEL*parallel_modify)) cur_best=all_diagnose_tree_local_new_opt(a_down_buf,reroot_array[l],ntax,ntax,values,0,corres);
else cur_best=all_diagnose_tree_local_parallel_new_opt(a_down_buf,reroot_array[l],ntax,ntax,values,0,corres);
}
if (!values->new_optimization && (score_holder>0)) {
values->phylo_score=score_holder;
cur_best=a_down_buf[reroot_array[l][0][1]]->score=cladogram(a_down_buf[reroot_array[l][0][1]],values);
values->phylo_score=0;
}
/*for (x=0;x<ntax-1;x++) if (!(PARALLEL*parallel_modify)) fprintf(stderr,"%d %d,",reroot_array[l][x][0],reroot_array[l][x][1]);
if (!(PARALLEL*parallel_modify)) fprintf(stderr,"%d\n",cur_best);*/
/*compare etc*/
if (cur_best < tot_best) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr," Found better at %d (R)\n",cur_best);
tot_best=cur_best;
found_better=1;
for (k=0;k<ntax-1;k++) {
best_nodes_new[0][k][0]=reroot_array[l][k][0];
best_nodes_new[0][k][1]=reroot_array[l][k][1];
}
/*add best_aligns stuf free first*/
for (k=0;k<tree_counter;k++) if (best_aligns[k]) best_aligns[k]=dump_align(best_aligns[k]);
best_aligns[0]=make_align(a_down_buf[reroot_array[l][0][1]]);
if (values->new_optimization && (values->collapse != 2)) {
/*redo name for collapse*/
if (!mult) check=get_collapsed_thang(best_aligns[0],best_nodes_new[0],ntax,check_buf,PARALLEL*parallel_modify*1,values);
else check=get_collapsed_thang_with_groups_old(best_aligns[0],best_nodes_new[0],ntax,check_buf,PARALLEL*parallel_modify*1,values,values->support[0]);
best_aligns[0]->score=tot_best;
}
tree_counter=1;
}
else if ((cur_best == tot_best) && mult && (tree_counter< values->keep_aligns)) {
for (k=0;k<ntax-1;k++) {
best_nodes_new[tree_counter][k][0]=reroot_array[l][k][0];
best_nodes_new[tree_counter][k][1]=reroot_array[l][k][1];
}
/*chec to see if novel*/
is_unique=1;
if (!values->new_optimization) for (k=0;k<tree_counter;k++) is_unique*=compare_aligns(a_down_buf[reroot_array[l][0][1]],best_aligns[k]);
else {
if (values->collapse==2) is_unique=is_unique_tree(best_nodes_new[tree_counter],best_nodes_new,tree_counter,best_nodes_old,cur_num_trees,old_length,tot_best,ntax);
else is_unique=is_unique_tree_align(best_aligns,best_nodes_new[tree_counter],best_nodes_new,tree_counter,best_nodes_old,cur_num_trees,old_length,tot_best,ntax,check_buf,PARALLEL*parallel_modify*1,values,collapse_name);
}