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nodes11.c
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nodes11.c
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/*Copyright 1994 Ward Wheeler all rights reserved*/
/*ned to add something which will pic individual taxa and move them as well*/
#include "align3.h"
realloc_align_holder *do_node_swap(counter,old_rep,a,best_aligns,nodes,n_nodes,l,values,current,ntaxa,align_passer)
int *counter, **old_rep, **nodes, **n_nodes,*l;
int ntaxa,current;
parameters *values;
alignment **a,**best_aligns;
realloc_align_holder *align_passer;
{
int i,j,k,m,sub_taxa,found_how_many,ii;
int cur_val,best_value,**tree_rep;
char overflow,temp,found_better_or_more;
int *intermediate_scores,intermediate_best_score, ***intermediate_nodes;
int ***best_nodes;
alignment **intermediate_align;
int num_intermediates_allocated;
int num_best_aligns, next_to_do, num_actually_done;
int bufid, bytes, type, source, max_to_do, index, grain=1, num_left, info, n_sub_taxa;
int ***from_nodes, **new_node, current_from[2], *is_descendent, **yet_newer_node, kk;
int kkk, found_new, ***node_counter, old_number_best, n_left, n_plucked;
int **remain_node, **prune_node, **unrooted_prune_node, **block_node, **new_prune_node;
int root, *is_descendent2, root_node, root_desc, num_spots,jj,lll,ll;
int *is_descendent3, root_node_root,root_desc_root, num_spots_root;
int **remain_node_root, **prune_node_root, **unrooted_prune_node_root, **block_node_root;
int **new_prune_node_root;
int **new_node_root,**yet_newer_node_root, checker, test_score,jjj;
int **cur_groups, test, ngroups2;
int number_sent, number_recieved,i1,j1,i2;
int doit,single_anc;
sub_taxa=current+4;
best_value=intermediate_best_score=best_aligns[0]->score;
new_node=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)new_node);
for (i=0;i<(ntaxa-1);i++) {
new_node[i]=(int *)malloc(2*sizeof(int));
assert((int) new_node[i]);
}
new_node_root=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)new_node_root);
for (i=0;i<(ntaxa-1);i++) {
new_node_root[i]=(int *)malloc(2*sizeof(int));
assert((int) new_node_root[i]);
}
yet_newer_node=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)yet_newer_node);
for (i=0;i<(ntaxa-1);i++) {
yet_newer_node[i]=(int *)malloc(2*sizeof(int));
assert((int) yet_newer_node[i]);
}
remain_node=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)remain_node);
prune_node=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)prune_node);
unrooted_prune_node=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)unrooted_prune_node);
block_node=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)block_node);
new_prune_node=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)new_prune_node);
for (i=0;i<(ntaxa-1);i++) {
remain_node[i]=(int *)malloc(2*sizeof(int));
assert((int) remain_node[i]);
prune_node[i]=(int *)malloc(2*sizeof(int));
assert((int) prune_node[i]);
unrooted_prune_node[i]=(int *)malloc(3*sizeof(int));
assert((int) unrooted_prune_node[i]);
block_node[i]=(int *)malloc(3*sizeof(int));
assert((int) block_node[i]);
new_prune_node[i]=(int *)malloc(2*sizeof(int));
assert((int) new_prune_node[i]);
}
remain_node_root=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)remain_node_root);
prune_node_root=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)prune_node_root);
unrooted_prune_node_root=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)unrooted_prune_node_root);
block_node_root=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)block_node_root);
new_prune_node_root=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)new_prune_node_root);
for (i=0;i<(ntaxa-1);i++) {
remain_node_root[i]=(int *)malloc(2*sizeof(int));
assert((int) remain_node_root[i]);
prune_node_root[i]=(int *)malloc(2*sizeof(int));
assert((int) prune_node_root[i]);
unrooted_prune_node_root[i]=(int *)malloc(3*sizeof(int));
assert((int) unrooted_prune_node_root[i]);
block_node_root[i]=(int *)malloc(3*sizeof(int));
assert((int) block_node_root[i]);
new_prune_node_root[i]=(int *)malloc(2*sizeof(int));
assert((int) new_prune_node_root[i]);
}
is_descendent=(int *)malloc(((2*ntaxa)-1)*sizeof(int));
assert((int) is_descendent);
is_descendent2=(int *)malloc(((2*ntaxa)-1)*sizeof(int));
assert((int) is_descendent2);
is_descendent3=(int *)malloc(((2*ntaxa)-1)*sizeof(int));
assert((int) is_descendent3);
for (i=1;i<((2*ntaxa)-1);i++) is_descendent3[i]=1;
is_descendent3[0]=0;
num_intermediates_allocated=1;
intermediate_scores=(int *)malloc(num_intermediates_allocated*sizeof(int));
assert((int) intermediate_scores);
intermediate_align=(alignment **)malloc(num_intermediates_allocated*sizeof(alignment *));
assert((int) intermediate_align);
intermediate_nodes=(int ***)malloc(num_intermediates_allocated*sizeof(int **));
assert((int) intermediate_nodes);
for (i=0;i<num_intermediates_allocated;i++) {
intermediate_align[i]=NULL;
intermediate_nodes[i]=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int) intermediate_nodes[i]);
for (j=0;j<(ntaxa-1);j++) {
intermediate_nodes[i][j]=(int *)malloc(2*sizeof(int));
assert((int) intermediate_nodes[i][j]);
}
}
best_nodes=(int ***)malloc(values->keep_aligns*sizeof(int **));
assert((int) best_nodes);
for (i=0;i<values->keep_aligns;i++) {
best_nodes[i]=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int) best_nodes[i]);
for (j=0;j<(ntaxa-1);j++) {
best_nodes[i][j]=(int *)malloc(2*sizeof(int));
assert((int) best_nodes[i][j]);
}
}
node_counter=(int ***)malloc(values->keep_aligns*sizeof(int **));
assert((int) node_counter);
for (i=0;i<values->keep_aligns;i++) {
node_counter[i]=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int) node_counter[i]);
for (j=0;j<(ntaxa-1);j++) {
node_counter[i][j]=(int *)malloc(2*sizeof(int));
assert((int) node_counter[i][j]);
}
}
if ((values->ngroups>0) && (values->groups_as_start)) {
for (i=0;i<values->ngroups;i++) free(values->groups[i]);
free(values->groups);
values->groups=NULL;
values->ngroups=0;
fprintf(stderr," Freeing groups\n");
if (PARALLEL) pvm_mcast(&(values->tids[1]),values->num_hosts-1, PVM_DUMP_INITIAL_GROUPS);
}
for (i=0;i<=(*counter);i++) all_other_make_nodes3(old_rep[i],ntaxa,sub_taxa,best_nodes[i]);
old_number_best=0;
found_how_many=0;
node_top:
;
if (values->VERBOSE) {
fprintf(stderr,"(node swapping");
fflush(stderr);
}
overflow=found_better_or_more=found_new=0;
/*nodes_to_swap=0;*/
for (i=0;i<=(*counter);i++) copy_nodes(ntaxa,sub_taxa,best_nodes[i],node_counter[i]);
for (i=old_number_best;i<=(*counter);i++) {/*swap on input tree_reps*/
copy_nodes(ntaxa,sub_taxa,node_counter[i],n_nodes);
for (j=0;j<num_intermediates_allocated;j++) if (intermediate_align[j]) intermediate_align[j]=dump_align(intermediate_align[j]);
ii=-1;
if (PARALLEL) number_sent=number_recieved=0;
for (j=1;j<sub_taxa;j++) {
n_left=sub_taxa-1;
n_plucked=1;
/*for each node > 0 with remaing taxa >1 pick node and create new nodes description*/
/*these next two yield TBR root after adding the swanstucker (maybe get all any way and more efficient)
could do rerootings of remainder - better to do after addition to get full roots of pruned bit
could do rerootings of pruned bit*/
for (k=0;k<sub_taxa-1;k++) {
if (n_nodes[k][0]==j) single_anc=k;
else if (n_nodes[k][1]==j) single_anc=k;
}
pick_node_and_remake_with_from(ntaxa,sub_taxa,n_nodes,j,new_node,current_from);
for (k=0;k<sub_taxa-1;k++) for (kk=0;kk<2;kk++) {
/*generate new node insertions*/
if (!((k==0) && (kk==0))) if (!((k==current_from[0]) && (kk==current_from[1]))) if (k!=single_anc) {
/*fprintf(stderr,"New node:\n"); print_nodes(ntaxa,sub_taxa,new_node);
fprintf(stderr,"CF0=%d CF1=%d\n",current_from[0],current_from[1]);*/
get_new_topo( ntaxa,sub_taxa,j,new_node,yet_newer_node,k, kk);
/*fprintf(stderr,"- ");
fprintf(stderr,"Yet newer:\n"); print_nodes(ntaxa,sub_taxa,yet_newer_node);*/
checker=1;
if (!checker) {
fprintf(stderr,"AAAH! problems!\n");
printf("AAAH! problems!\n");
printf("Unrooted prune node root\n");
print_nodes3_stdout(ntaxa,sub_taxa,unrooted_prune_node_root);
printf("New prune node root\n");
print_nodes3_stdout(ntaxa,sub_taxa,new_prune_node_root);
printf("New node root\n");
print_nodes_stdout(ntaxa,sub_taxa,new_node_root);
printf("Yet Newer node\n");
print_nodes_stdout(ntaxa,sub_taxa,yet_newer_node);
}
else {
/*get alignment*/
if (PARALLEL && !SPECIAL) {
/*insert topology test here if (!values->groups) */
doit=1;
if (doit) {
if (number_sent < (values->num_hosts-1)) {
/* code folded from here */
/*send out job*/
pvm_initsend(PvmDataDefault);
pvm_pkint(&grain,1,1);
pvm_pkint(&ntaxa,1,1);
for (i1=0;i1<ntaxa-1;i1++) for (j1=0;j1<2;j1++) pvm_pkint(&(yet_newer_node[i1][j1]),1,1);
pvm_send(values->tids[number_sent+1],PVM_REQUEST_DIAGNOSE_ALIGNMENT);
++number_sent;
/* unfolding */
}
else {
/* code folded from here */
/*blocking recieve*/
bufid=pvm_recv(-1,PVM_SEND_DIAGNOSE_ALIGNMENT);
if (bufid) {
info=pvm_bufinfo(bufid, &bytes, &type, &source);
/*send out next job*/
pvm_initsend(PvmDataDefault);
pvm_pkint(&grain,1,1);
pvm_pkint(&ntaxa,1,1);
for (i1=0;i1<ntaxa-1;i1++) for (j1=0;j1<2;j1++) pvm_pkint(&(yet_newer_node[i1][j1]),1,1);
pvm_send(source,PVM_REQUEST_DIAGNOSE_ALIGNMENT);
++number_sent;
/*unpack*/
++number_recieved;
pvm_upkint(&grain,1,1);
pvm_upkint(&test_score,1,1);
/*evaluate reallocate ii etc*/
if ((test_score<=intermediate_best_score) && (test_score!=HUGE_COST)) {
if (test_score<intermediate_best_score) {
if (ii>=num_intermediates_allocated-1) {
++num_intermediates_allocated;
intermediate_scores=(int *)realloc(intermediate_scores,num_intermediates_allocated*sizeof(int));
assert((int) intermediate_scores);
intermediate_align=(alignment **)realloc(intermediate_align,num_intermediates_allocated*sizeof(alignment *));
assert((int) intermediate_align);
intermediate_nodes=(int ***)realloc(intermediate_nodes,num_intermediates_allocated*sizeof(int **));
assert((int) intermediate_nodes);
intermediate_align[num_intermediates_allocated-1]=NULL;
intermediate_nodes[num_intermediates_allocated-1]=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int) intermediate_nodes[num_intermediates_allocated-1]);
for (jjj=0;jjj<(ntaxa-1);jjj++) {
intermediate_nodes[num_intermediates_allocated-1][jjj]=(int *)malloc(2*sizeof(int));
assert((int) intermediate_nodes[num_intermediates_allocated-1][jjj]);
}
}
intermediate_scores[++ii]=test_score;
intermediate_best_score=intermediate_scores[ii];
if (values->VERBOSE) fprintf(stderr,"Found better at cost %d.\n",intermediate_best_score);
if (intermediate_align[ii]) intermediate_align[ii]=dump_align(intermediate_align[ii]);
intermediate_align[ii]=unpack_align(test_score,values);
/*unpack nodes*/
for (i1=0;i1<ntaxa-1;i1++) for (j1=0;j1<2;j1++) pvm_upkint(&(intermediate_nodes[ii][i1][j1]),1,1);
}
else if (!values->aquick) {
if (ii>=num_intermediates_allocated-1) {
++num_intermediates_allocated;
intermediate_scores=(int *)realloc(intermediate_scores,num_intermediates_allocated*sizeof(int));
assert((int) intermediate_scores);
intermediate_align=(alignment **)realloc(intermediate_align,num_intermediates_allocated*sizeof(alignment *));
assert((int) intermediate_align);
intermediate_nodes=(int ***)realloc(intermediate_nodes,num_intermediates_allocated*sizeof(int **));
assert((int) intermediate_nodes);
intermediate_align[num_intermediates_allocated-1]=NULL;
intermediate_nodes[num_intermediates_allocated-1]=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int) intermediate_nodes[num_intermediates_allocated-1]);
for (jjj=0;jjj<(ntaxa-1);jjj++) {
intermediate_nodes[num_intermediates_allocated-1][jjj]=(int *)malloc(2*sizeof(int));
assert((int) intermediate_nodes[num_intermediates_allocated-1][jjj]);
}
}
intermediate_scores[++ii]=test_score;
if (intermediate_align[ii]) intermediate_align[ii]=dump_align(intermediate_align[ii]);
intermediate_align[ii]=unpack_align(test_score,values);
/*unpack_nodes*/
for (i1=0;i1<ntaxa-1;i1++) for (j1=0;j1<2;j1++) pvm_upkint(&(intermediate_nodes[ii][i1][j1]),1,1);
}
}
}
/* unfolding */
}
}
}
else { /*not parallel*/
/* insert topology test here */
if (!values->groups) test_score=all_diagnose_tree(a,yet_newer_node,
ntaxa,sub_taxa,values);
else {
cur_groups=get_cur_groups(yet_newer_node,ntaxa,sub_taxa,&ngroups2);
test=compare_groups(values->groups,cur_groups,values->ngroups,
ngroups2,ntaxa-1,sub_taxa-1);
/*dump groups*/
for (i=0;i<ngroups2;i++) free(cur_groups[i]);
free(cur_groups);
if (!test) test_score=HUGE_COST;
else test_score=all_diagnose_tree(a,yet_newer_node,ntaxa,
sub_taxa,values);
}
/*fprintf(stderr,"\n");*/
if (test_score<=intermediate_best_score) {
if (test_score<intermediate_best_score) {
/* code folded from here */
if (ii>=num_intermediates_allocated-1) {
++num_intermediates_allocated;
intermediate_scores=(int *)realloc(intermediate_scores,num_intermediates_allocated*sizeof(int));
assert((int) intermediate_scores);
intermediate_align=(alignment **)realloc(intermediate_align,num_intermediates_allocated*sizeof(alignment *));
assert((int) intermediate_align);
intermediate_nodes=(int ***)realloc(intermediate_nodes,num_intermediates_allocated*sizeof(int **));
assert((int) intermediate_nodes);
intermediate_align[num_intermediates_allocated-1]=NULL;
intermediate_nodes[num_intermediates_allocated-1]=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int) intermediate_nodes[num_intermediates_allocated-1]);
for (jjj=0;jjj<(ntaxa-1);jjj++) {
intermediate_nodes[num_intermediates_allocated-1][jjj]=(int *)malloc(2*sizeof(int));
assert((int) intermediate_nodes[num_intermediates_allocated-1][jjj]);
}
}
intermediate_scores[++ii]=test_score;
intermediate_best_score=intermediate_scores[ii];
if (values->VERBOSE) fprintf(stderr,"Found better at cost %d.\n",intermediate_best_score);
if (intermediate_align[ii]) intermediate_align[ii]=dump_align(intermediate_align[ii]);
intermediate_align[ii]=make_align(a[yet_newer_node[0][1]]);
copy_nodes(ntaxa,sub_taxa,yet_newer_node,intermediate_nodes[ii]);
/* unfolding */
}
else if (!values->aquick) {
/* code folded from here */
if (ii>=num_intermediates_allocated-1) {
++num_intermediates_allocated;
intermediate_scores=(int *)realloc(intermediate_scores,num_intermediates_allocated*sizeof(int));
assert((int) intermediate_scores);
intermediate_align=(alignment **)realloc(intermediate_align,num_intermediates_allocated*sizeof(alignment *));
assert((int) intermediate_align);
intermediate_nodes=(int ***)realloc(intermediate_nodes,num_intermediates_allocated*sizeof(int **));
assert((int) intermediate_nodes);
intermediate_align[num_intermediates_allocated-1]=NULL;
intermediate_nodes[num_intermediates_allocated-1]=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int) intermediate_nodes[num_intermediates_allocated-1]);
for (jjj=0;jjj<(ntaxa-1);jjj++) {
intermediate_nodes[num_intermediates_allocated-1][jjj]=(int *)malloc(2*sizeof(int));
assert((int) intermediate_nodes[num_intermediates_allocated-1][jjj]);
}
}
intermediate_scores[++ii]=test_score;
if (intermediate_align[ii]) intermediate_align[ii]=dump_align(intermediate_align[ii]);
intermediate_align[ii]=make_align(a[yet_newer_node[0][1]]);
copy_nodes(ntaxa,sub_taxa,yet_newer_node,intermediate_nodes[ii]);
/* unfolding */
}
}
}
}
/* unfolding */
/* unfolding */
/* unfolding */
/* unfolding */
}
}/*TBR loop*/
}/*picked j*/
/*nodes with more than a single descendent taxon*/
for (j=1+ntaxa;j<sub_taxa-1+ntaxa;j++) {
n_left=remainder(n_nodes,ntaxa,sub_taxa,j-ntaxa,is_descendent,is_descendent2);
n_plucked=sub_taxa-n_left;
if (n_left>1) {
/*for each node > 0 with remaing taxa >1 pick node and create new nodes description*/
/*these next two yield TBR root after adding the swanstucker (maybe get all any way and more efficient)
could do rerootings of remainder - better to do after addition to get full roots of pruned bit
could do rerootings of pruned bit*/
pick_node_and_remake_with_from(ntaxa,sub_taxa,n_nodes,j,new_node,current_from);
if ((values->align_root_swap) && (n_plucked>2)) {
split_nodes(ntaxa,sub_taxa,new_node,remain_node,prune_node,is_descendent2);
unroot_pruned(ntaxa,sub_taxa,prune_node,unrooted_prune_node,is_descendent2,&root_node,
&root_desc);
block_redundant_additions(ntaxa,sub_taxa,unrooted_prune_node,block_node,is_descendent2,
root_node,root_desc);
num_spots=0;
for (jj=0;jj<sub_taxa-1;jj++) for (k=0;k<3;k++) if (!block_node[jj][k]) ++num_spots;
if (num_spots==0) num_spots=1;
}
else num_spots=1;
for (jj=0;jj<num_spots;jj++) {
if ((values->align_root_swap) && (n_plucked>2) && (num_spots>1)) {
pick_new_root(ntaxa,sub_taxa,unrooted_prune_node,block_node,jj+1,new_prune_node,
is_descendent2,root_node,root_desc);
/*copy_nodes(ntaxa,sub_taxa,prune_node,new_prune_node);*/
remake_nodes(ntaxa,sub_taxa,remain_node,new_prune_node,new_node,is_descendent2);
/*fprintf(stderr,"Remade:\n");
print_nodes(ntaxa,sub_taxa,new_node);*/
}
for (k=0;k<sub_taxa-1;k++) {
for (kk=0;kk<2;kk++) if ((!is_descendent[new_node[k][kk]])) {
/*generate new node insertions*/
if (!((k==0) && (kk==0))) if (!((k==current_from[0]) && (current_from[1]!=kk))) {
/*fprintf(stderr,"New node:\n");
print_nodes(ntaxa,sub_taxa,new_node);*/
get_new_topo( ntaxa,sub_taxa,j,new_node,yet_newer_node,k,
kk);
/*fprintf(stderr,"Yet newer:\n");
print_nodes(ntaxa,sub_taxa,yet_newer_node);*/
if ((values->align_complete_root_swap) || (values->align_partial_root_swap)) {
/* code folded from here */
split_nodes(ntaxa,sub_taxa,yet_newer_node,remain_node_root,
prune_node_root,is_descendent3);
unroot_pruned(ntaxa,sub_taxa,prune_node_root,unrooted_prune_node_root,is_descendent3,&root_node_root,&root_desc_root);
if (!values->align_partial_root_swap) block_redundant_additions(ntaxa,sub_taxa,unrooted_prune_node_root,block_node_root,is_descendent3,root_node_root,root_desc_root);
else block_redundant_additions_and_non_pruned(ntaxa,sub_taxa,unrooted_prune_node_root,block_node_root,is_descendent3,root_node_root,root_desc_root,is_descendent);
num_spots_root=0;
for (ll=0;ll<sub_taxa-1;ll++) for (lll=0;lll<3;lll++) if (block_node_root[ll][lll]==0) ++num_spots_root;
if (num_spots_root==0) num_spots_root=1;
/* unfolding */
}
else num_spots_root=1;
if (values->align_partial_root_swap) ++num_spots_root;/*this so do original root + the rootings in the pruned group*/
/*if (j<ntaxa) num_spots_root=0;*/
for (ll=0;ll<num_spots_root;ll++) {
/* code folded from here */
if (!((values->align_partial_root_swap) && (ll==(num_spots_root-1)))) {
/*put loop here to reroot each addition=rooted TBR*/
if (values->align_complete_root_swap && (num_spots_root>1)) {
pick_new_root(ntaxa,sub_taxa,unrooted_prune_node_root,block_node_root,ll+1,new_prune_node_root,is_descendent3,root_node_root,root_desc_root);
remake_nodes(ntaxa,sub_taxa,remain_node_root,new_prune_node_root,new_node_root,is_descendent3);
/*print_nodes(ntaxa,sub_taxa,new_node_root);*/
copy_nodes(ntaxa,sub_taxa,new_node_root,yet_newer_node);
yet_newer_node[0][0]=0;
}
}
checker=1;
if (!checker) {
fprintf(stderr,"AAAH! problems!\n");
printf("AAAH! problems!\n");
printf("Unrooted prune node root\n");
print_nodes3_stdout(ntaxa,sub_taxa,unrooted_prune_node_root);
printf("New prune node root\n");
print_nodes3_stdout(ntaxa,sub_taxa,new_prune_node_root);
printf("New node root\n");
print_nodes_stdout(ntaxa,sub_taxa,new_node_root);
printf("Yet Newer node\n");
print_nodes_stdout(ntaxa,sub_taxa,yet_newer_node);
}
else {
/*get alignment*/
if (PARALLEL) {
/* code folded from here */
doit=1;
/* code folded from here */
if (doit) {
if (number_sent < (values->num_hosts-1)) {
/*send out job*/
pvm_initsend(PvmDataDefault);
pvm_pkint(&grain,1,1);
pvm_pkint(&ntaxa,1,1);
for (i1=0;i1<ntaxa-1;i1++) for (j1=0;j1<2;j1++) pvm_pkint(&(yet_newer_node[i1][j1]),1,1);
pvm_send(values->tids[number_sent+1],PVM_REQUEST_DIAGNOSE_ALIGNMENT);
++number_sent;
}
else {
/*blocking recieve*/
bufid=pvm_recv(-1,PVM_SEND_DIAGNOSE_ALIGNMENT);
if (bufid) {
info=pvm_bufinfo(bufid, &bytes, &type, &source);
/*send out next job*/
pvm_initsend(PvmDataDefault);
pvm_pkint(&grain,1,1);
pvm_pkint(&ntaxa,1,1);
for (i1=0;i1<ntaxa-1;i1++) for (j1=0;j1<2;j1++) pvm_pkint(&(yet_newer_node[i1][j1]),1,1);
pvm_send(source,PVM_REQUEST_DIAGNOSE_ALIGNMENT);
++number_sent;
/*unpack*/
++number_recieved;
pvm_upkint(&grain,1,1);
pvm_upkint(&test_score,1,1);
/*evaluate reallocate ii etc*/
if ((test_score<=intermediate_best_score) && (test_score!=HUGE_COST)) {
if (test_score<intermediate_best_score) {
if (ii>=num_intermediates_allocated-1) {
++num_intermediates_allocated;
intermediate_scores=(int *)realloc(intermediate_scores,num_intermediates_allocated*sizeof(int));
assert((int) intermediate_scores);
intermediate_align=(alignment **)realloc(intermediate_align,num_intermediates_allocated*sizeof(alignment *));
assert((int) intermediate_align);
intermediate_nodes=(int ***)realloc(intermediate_nodes,num_intermediates_allocated*sizeof(int **));
assert((int) intermediate_nodes);
intermediate_align[num_intermediates_allocated-1]=NULL;
intermediate_nodes[num_intermediates_allocated-1]=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int) intermediate_nodes[num_intermediates_allocated-1]);
for (jjj=0;jjj<(ntaxa-1);jjj++) {
intermediate_nodes[num_intermediates_allocated-1][jjj]=(int *)malloc(2*sizeof(int));
assert((int) intermediate_nodes[num_intermediates_allocated-1][jjj]);
}
}
intermediate_scores[++ii]=test_score;
intermediate_best_score=intermediate_scores[ii];
if (values->VERBOSE) fprintf(stderr,"Found better at cost %d.\n",intermediate_best_score);
if (intermediate_align[ii]) intermediate_align[ii]=dump_align(intermediate_align[ii]);
intermediate_align[ii]=unpack_align(test_score,values);
/*unpack nodes*/
for (i1=0;i1<ntaxa-1;i1++) for (j1=0;j1<2;j1++) pvm_upkint(&(intermediate_nodes[ii][i1][j1]),1,1);
}
else if (!values->aquick) {
if (ii>=num_intermediates_allocated-1) {
++num_intermediates_allocated;
intermediate_scores=(int *)realloc(intermediate_scores,num_intermediates_allocated*sizeof(int));
assert((int) intermediate_scores);
intermediate_align=(alignment **)realloc(intermediate_align,num_intermediates_allocated*sizeof(alignment *));
assert((int) intermediate_align);
intermediate_nodes=(int ***)realloc(intermediate_nodes,num_intermediates_allocated*sizeof(int **));
assert((int) intermediate_nodes);
intermediate_align[num_intermediates_allocated-1]=NULL;
intermediate_nodes[num_intermediates_allocated-1]=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int) intermediate_nodes[num_intermediates_allocated-1]);
for (jjj=0;jjj<(ntaxa-1);jjj++) {
intermediate_nodes[num_intermediates_allocated-1][jjj]=(int *)malloc(2*sizeof(int));
assert((int) intermediate_nodes[num_intermediates_allocated-1][jjj]);
}
}
intermediate_scores[++ii]=test_score;
if (intermediate_align[ii]) intermediate_align[ii]=dump_align(intermediate_align[ii]);
intermediate_align[ii]=unpack_align(test_score,values);
/*unpack_nodes*/
for (i1=0;i1<ntaxa-1;i1++) for (j1=0;j1<2;j1++) pvm_upkint(&(intermediate_nodes[ii][i1][j1]),1,1);
}
}
}
}
}
}
else {
/* insert topology test here */
if (!values->groups) test_score=all_diagnose_tree(a,yet_newer_node,ntaxa,sub_taxa,values);
else {
cur_groups=get_cur_groups(yet_newer_node,ntaxa,sub_taxa,&ngroups2);
test=compare_groups(values->groups,cur_groups,values->ngroups,ngroups2,ntaxa-1,sub_taxa-1);
/*dump groups*/
for (i=0;i<ngroups2;i++) free(cur_groups[i]);
free(cur_groups);
if (!test) test_score=HUGE_COST;
else test_score=all_diagnose_tree(a,yet_newer_node,ntaxa,sub_taxa,values);
}
/*fprintf(stderr,"\n");*/
if (test_score<=intermediate_best_score) {
if (test_score<intermediate_best_score) {
if (ii>=num_intermediates_allocated-1) {
++num_intermediates_allocated;
intermediate_scores=(int *)realloc(intermediate_scores,num_intermediates_allocated*sizeof(int));
assert((int) intermediate_scores);
intermediate_align=(alignment **)realloc(intermediate_align,num_intermediates_allocated*sizeof(alignment *));
assert((int) intermediate_align);
intermediate_nodes=(int ***)realloc(intermediate_nodes,num_intermediates_allocated*sizeof(int **));
assert((int) intermediate_nodes);
intermediate_align[num_intermediates_allocated-1]=NULL;
intermediate_nodes[num_intermediates_allocated-1]=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int) intermediate_nodes[num_intermediates_allocated-1]);
for (jjj=0;jjj<(ntaxa-1);jjj++) {
intermediate_nodes[num_intermediates_allocated-1][jjj]=(int *)malloc(2*sizeof(int));
assert((int) intermediate_nodes[num_intermediates_allocated-1][jjj]);
}
}
intermediate_scores[++ii]=test_score;
intermediate_best_score=intermediate_scores[ii];
if (values->VERBOSE) fprintf(stderr,"Found better at cost %d.\n",intermediate_best_score);
if (intermediate_align[ii]) intermediate_align[ii]=dump_align(intermediate_align[ii]);
intermediate_align[ii]=make_align(a[yet_newer_node[0][1]]);
copy_nodes(ntaxa,sub_taxa,yet_newer_node,intermediate_nodes[ii]);
}
else if (!values->aquick) {
if (ii>=num_intermediates_allocated-1) {
++num_intermediates_allocated;
intermediate_scores=(int *)realloc(intermediate_scores,num_intermediates_allocated*sizeof(int));
assert((int) intermediate_scores);
intermediate_align=(alignment **)realloc(intermediate_align,num_intermediates_allocated*sizeof(alignment *));
assert((int) intermediate_align);
intermediate_nodes=(int ***)realloc(intermediate_nodes,num_intermediates_allocated*sizeof(int **));
assert((int) intermediate_nodes);
intermediate_align[num_intermediates_allocated-1]=NULL;
intermediate_nodes[num_intermediates_allocated-1]=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int) intermediate_nodes[num_intermediates_allocated-1]);
for (jjj=0;jjj<(ntaxa-1);jjj++) {
intermediate_nodes[num_intermediates_allocated-1][jjj]=(int *)malloc(2*sizeof(int));
assert((int) intermediate_nodes[num_intermediates_allocated-1][jjj]);
}
}
intermediate_scores[++ii]=test_score;
if (intermediate_align[ii]) intermediate_align[ii]=dump_align(intermediate_align[ii]);
intermediate_align[ii]=make_align(a[yet_newer_node[0][1]]);
copy_nodes(ntaxa,sub_taxa,yet_newer_node,intermediate_nodes[ii]);
}
}
}
}
/* unfolding */
/* unfolding */
/* unfolding */
/* unfolding */
/* unfolding */
}
}
} /*if (!descendent)*/
}/*TBR loop*/
}
}
}/*picked j*/
if (PARALLEL) {
/*get the reaminder of jobs not recieved (this should always be values->num_hosts-2)*/
while (number_recieved< number_sent) {
/*blocking recieve*/
bufid=pvm_recv(-1,PVM_SEND_DIAGNOSE_ALIGNMENT);
if (bufid) {
info=pvm_bufinfo(bufid, &bytes, &type, &source);
/*unpack*/
++number_recieved;
pvm_upkint(&grain,1,1);
pvm_upkint(&test_score,1,1);
/*evaluate reallocate ii etc*/
if ((test_score<=intermediate_best_score) && (test_score!=HUGE_COST)) {
if (test_score<intermediate_best_score) {
if (ii>=num_intermediates_allocated-1) {
++num_intermediates_allocated;
intermediate_scores=(int *)realloc(intermediate_scores,num_intermediates_allocated*sizeof(int));
assert((int) intermediate_scores);
intermediate_align=(alignment **)realloc(intermediate_align,
num_intermediates_allocated*sizeof(alignment *));
assert((int) intermediate_align);
intermediate_nodes=(int ***)realloc(intermediate_nodes,num_intermediates_allocated*sizeof(int
**));
assert((int) intermediate_nodes);
intermediate_align[num_intermediates_allocated-1]=NULL;
intermediate_nodes[num_intermediates_allocated-1]=(int **)malloc((ntaxa-1)*sizeof(int
*));
assert((int) intermediate_nodes[num_intermediates_allocated-1]);
for (jjj=0;jjj<(ntaxa-1);jjj++) {
/* code folded from here */
/* code folded from here */
intermediate_nodes[num_intermediates_allocated-1][jjj]=(int
*)malloc(2*sizeof(int));
assert((int) intermediate_nodes[num_intermediates_allocated-1][jjj]);
/* unfolding */
/* unfolding */
}
}
intermediate_scores[++ii]=test_score;
intermediate_best_score=intermediate_scores[ii];
if (values->VERBOSE) fprintf(stderr,"Found better at cost %d.\n",
intermediate_best_score);
if (intermediate_align[ii]) intermediate_align[ii]=dump_align(intermediate_align[ii]);
intermediate_align[ii]=unpack_align(test_score,values);
/*unpack nodes*/
for (i1=0;i1<ntaxa-1;i1++) for (j1=0;j1<2;j1++) pvm_upkint(&(intermediate_nodes[ii][i1][j1]),
1,1);
}
else if (!values->aquick) {
if (ii>=num_intermediates_allocated-1) {
++num_intermediates_allocated;
intermediate_scores=(int *)realloc(intermediate_scores,num_intermediates_allocated*sizeof(int));
assert((int) intermediate_scores);
intermediate_align=(alignment **)realloc(intermediate_align,
num_intermediates_allocated*sizeof(alignment *));
assert((int) intermediate_align);
intermediate_nodes=(int ***)realloc(intermediate_nodes,num_intermediates_allocated*sizeof(int
**));
assert((int) intermediate_nodes);
intermediate_align[num_intermediates_allocated-1]=NULL;
intermediate_nodes[num_intermediates_allocated-1]=(int **)malloc((ntaxa-1)*sizeof(int
*));
assert((int) intermediate_nodes[num_intermediates_allocated-1]);
for (jjj=0;jjj<(ntaxa-1);jjj++) {
/* code folded from here */
/* code folded from here */
intermediate_nodes[num_intermediates_allocated-1][jjj]=(int
*)malloc(2*sizeof(int));
assert((int) intermediate_nodes[num_intermediates_allocated-1][jjj]);
/* unfolding */
/* unfolding */
}
}
intermediate_scores[++ii]=test_score;
if (intermediate_align[ii]) intermediate_align[ii]=dump_align(intermediate_align[ii]);
intermediate_align[ii]=unpack_align(test_score,values);
/*unpack_nodes*/
for (i1=0;i1<ntaxa-1;i1++) for (j1=0;j1<2;j1++) pvm_upkint(&(intermediate_nodes[ii][i1][j1]),
1,1);
}
}
}/*recieve*/
}
}
/*loop through all alignments and scores to find good ones*/
num_best_aligns=0;
num_actually_done=ii+1;
/*fprintf(stderr,"Num actually done %d\n",num_actually_done);*/
for (j=0;j<num_actually_done;j++) if (intermediate_scores[j]==intermediate_best_score) ++num_best_aligns;
if ((best_value>intermediate_best_score) || (num_best_aligns>0)) { /*see if swap did anything*/
if (intermediate_best_score < best_value) {
best_value=intermediate_best_score;
for (k=0;k<(*l);k++) if (best_aligns[k]) best_aligns[k]=dump_align(best_aligns[k]);
(*l)=0;
found_new=1;
}
/*change all this rep shit to nodes*/
for (j=0;j<num_actually_done;j++) if ((intermediate_scores[j]==intermediate_best_score) && (intermediate_align[j])) {
if (!(*l)) {
found_better_or_more=1;
for (k=0;k<(*l);k++) if (best_aligns[k]) best_aligns[k]=dump_align(best_aligns[k]);
(*l)=1;
best_aligns[0]=make_align(intermediate_align[j]);
/*copy best and from*/
copy_nodes(ntaxa,sub_taxa,intermediate_nodes[j],best_nodes[0]);
}/*better*/
else if (!values->aquick) {
temp=1;
/*someday change compare aligns to supoprted nodes only difference*/
for (k=0;k<(*l);k++) if (best_aligns[k]) temp*=compare_aligns(intermediate_align[j],best_aligns[k]);
if (temp) {
if ((*l)>(values->keep_aligns-2)) {
if ((values->max_out_aligns) && ((best_aligns=(alignment **)realloc(best_aligns,(values->keep_aligns+1)*sizeof(alignment
*)))!=NULL) && ((best_nodes=(int ***)realloc(best_nodes,(values->keep_aligns+1)*sizeof(int **)))!=NULL) &&
((node_counter=(int ***)realloc(node_counter,(values->keep_aligns+1)*sizeof(int **)))!=NULL)) {
++values->keep_aligns;
best_aligns[values->keep_aligns-1]=NULL;
best_nodes[values->keep_aligns-1]=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)best_nodes[values->keep_aligns-1]);
for (k=0;k<ntaxa-1;k++) {
best_nodes[values->keep_aligns-1][k]=(int *)malloc(2*sizeof(int));
assert((int) best_nodes[values->keep_aligns-1][k]);
}
node_counter[values->keep_aligns-1]=(int **)malloc((ntaxa-1)*sizeof(int *));
assert((int)node_counter[values->keep_aligns-1]);
for (k=0;k<ntaxa-1;k++) {
node_counter[values->keep_aligns-1][k]=(int *)malloc(2*sizeof(int));
assert((int) node_counter[values->keep_aligns-1][k]);
}
}
}
if ((*l)>(values->keep_aligns-2)) {
if (!overflow) {
if (values->rep_error) fprintf(stderr,"Overflow in alignment node swap -- but that's OK.\n");
overflow=1;
}
}
else {
copy_nodes(ntaxa,sub_taxa,intermediate_nodes[j],best_nodes[(*l)]);
best_aligns[(*l)]=make_align(intermediate_align[j]);
++(*l);
found_better_or_more=1;
if (values->VERBOSE) fprintf(stderr,"Found another for %d alignments\n",(*l));
}
}
}/*additional*/
}
}
}
if (found_new) old_number_best=0;
else old_number_best=(*counter);
(*counter)=(*l)-1;
found_how_many+=found_better_or_more;
if (found_better_or_more) goto node_top;
for (i=0;i<(ntaxa-1);i++) {
free(new_prune_node[i]);
free(new_node[i]);
free(yet_newer_node[i]);
free(remain_node[i]);
free(prune_node[i]);
free(unrooted_prune_node[i]);
free(block_node[i]);
}
free(yet_newer_node);
free(new_node);
free(remain_node);
free(prune_node);
free(unrooted_prune_node);
free(block_node);
free(new_prune_node);
for (i=0;i<(ntaxa-1);i++) {
free(new_node_root[i]);
free(remain_node_root[i]);
free(prune_node_root[i]);
free(unrooted_prune_node_root[i]);
free(block_node_root[i]);
free(new_prune_node_root[i]);
}
free(new_node_root);
free(remain_node_root);
free(prune_node_root);
free(unrooted_prune_node_root);
free(block_node_root);
free(new_prune_node_root);
free(is_descendent);
free(is_descendent2);
free(is_descendent3);
free(intermediate_scores);
for (i=0;i<num_intermediates_allocated;i++) {
if (intermediate_align[i]) intermediate_align[i]=dump_align(intermediate_align[i]);
for (j=0;j<(ntaxa-1);j++) free(intermediate_nodes[i][j]);
free(intermediate_nodes[i]);
}
free(intermediate_align);
free(intermediate_nodes);
for (i=0;i<values->keep_aligns;i++) for (j=0;j<ntaxa-1;j++) {
free(best_nodes[i][j]);
free(node_counter[i][j]);
}
free(best_nodes);
free(node_counter);
if (values->VERBOSE) {
for (i=0;i<found_how_many;i++) fprintf(stderr,")");
fprintf(stderr,") ");
fflush(stderr);
}
align_passer->best=best_aligns;
align_passer->rep=old_rep;
return align_passer;
}
void all_other_make_nodes3(tree_rep,ntaxa,nent,node)
int **node;
int *tree_rep;
int ntaxa,nent;
{
int i,dummy1,dummy2;
/*node names start after the taxa*/
/*initialize nodes*/
node[0][0]=0;
node[0][1]=ntaxa+1;
node[1][0]=1;
node[1][1]=2;
for (i=3;i<nent;++i)
{
node[i-1][0]=i;
dummy1=(tree_rep[i-3])/2;
dummy2=(tree_rep[i-3])%2;
node[i-1][1]=node[dummy1][dummy2];
node[dummy1][dummy2]=ntaxa+i-1;
}
}
/*function to determine the number of taxa left after a pruning*/
int remainder(nodes,ntaxa,sub_taxa,node_taken,is_descendent,is_descendent2)
int node_taken, ntaxa, **nodes, *is_descendent, *is_descendent2;
{
int pruned,i;
int got_one, anc;
/*fprintf(stderr,"Getting remainder ");*/
/*how many descendents of node_taken?*/
for (i=0;i<((2*ntaxa)-1);i++) is_descendent[i]=0;
for (i=0;i<sub_taxa-1;i++) {
if (nodes[i][0]==(node_taken+ntaxa)) anc=i;
else if (nodes[i][1]==(node_taken+ntaxa)) anc=i;
}
is_descendent[node_taken+ntaxa]=1;
is_descendent[nodes[node_taken][0]]=1;
is_descendent[nodes[node_taken][1]]=1;
/*fprintf(stderr,"got fisrt ");*/
got_one=1;
while (got_one) {
got_one=0;
for (i=0;i<sub_taxa-1;i++){
/*fprintf(stderr,"%d ",i);*/
if (is_descendent[i+ntaxa]) {
if (!is_descendent[nodes[i][0]]) {
got_one=1;
is_descendent[nodes[i][0]]=1;
is_descendent[nodes[i][1]]=1;
}
}
}
}
/*fprintf(stderr,"done getting ");*/
/*for tbr stuff thats why not snc*/
is_descendent[anc+ntaxa]=1;
for (i=0;i<((2*ntaxa)-1);i++) is_descendent2[i]=is_descendent[i];
is_descendent[nodes[anc][0]]=1;
is_descendent[nodes[anc][1]]=1;
pruned=0;
for (i=0;i<sub_taxa;i++) pruned += is_descendent[i];
/*fprintf(stderr,"p-%d ",pruned);*/
return (sub_taxa-pruned);
}
void nodes_to_tree_rep(tree_rep,ntaxa,nent,node)
int **node;
int *tree_rep;
int ntaxa,nent;
{
int i,cur_i,cur_j,j,k;
int anc_i,anc_j, rep_count;
int temp_0,temp_1;
/*node names start after the taxa*/
/*for (i=3;i<nent;i++) {
node[i-1][0]=i;
dummy1=(tree_rep[i-3])/2;
dummy2=(tree_rep[i-3])%2;
node[i-1][1]=node[dummy1][dummy2];
node[dummy1][dummy2]=ntaxa+i-1;
}
*/
for (i=1;i<nent-1;i++) {
temp_0=node[i][0];
temp_1=node[i][1];
if (((temp_0<ntaxa) && (temp_1<ntaxa)) || ((temp_0>=ntaxa) && (temp_1>=ntaxa))) {
node[i][1]=min(temp_0,temp_1);
node[i][0]=max(temp_0,temp_1);
}
}
/*by taxa*/
for (i=nent-1;i>=3;i--) {
for (j=0;j<nent-1;j++) for (k=0;k<2;k++) if (node[j][k]==i) {
cur_i=j;
cur_j=k;
goto next;
}
next:
;
for (j=0;j<nent-1;j++) for (k=0;k<2;k++) if (node[j][k]==(ntaxa+cur_i)) {
anc_i=j;
anc_j=k;
goto still_next;
}
still_next:
;
node[anc_i][anc_j]=node[cur_i][!cur_j];
node[cur_i][cur_j]=HUGE_COST;
node[cur_i][!cur_j]=HUGE_COST;
rep_count=0;
for (j=0;j<nent-1;j++) for (k=0;k<2;k++) if (!((j==0) && (k==0))) {
if (node[j][k]<HUGE_COST) {
++rep_count;
if ((j==anc_i) && (k==anc_j)) goto still_more_next;
}
}
still_more_next:
;
tree_rep[i-3]=rep_count;
fprintf(stderr,"Iter %d\n",i);
print_nodes(ntaxa,nent,node);
}
for (i=0;i<nent-3;i++) fprintf(stderr,"tr[%d]=%d ",i,tree_rep[i]);
/*print_nodes(ntaxa,nent,node);*/
fprintf(stderr,"\n");
}
void pick_node_and_remake_with_from(ntaxa,sub_taxa,nodes,node_taken,new_node,from)
int ntaxa, sub_taxa, **nodes, node_taken, **new_node, *from;
{
int i, one_taken, anc_to_taken, one_not_taken;
/*copy to ne_node*/
for (i=0;i<(sub_taxa-1);i++) {
new_node[i][0]=nodes[i][0];
new_node[i][1]=nodes[i][1];
}
for (i=0;i<sub_taxa-1;i++) {
if ((new_node[i][0]==(node_taken)) || (new_node[i][1]==(node_taken))) {
if (new_node[i][0]==(node_taken)) {
one_taken=0;
one_not_taken=1;
}
else if (new_node[i][1]==(node_taken)) {
one_taken=1;
one_not_taken=0;
}
anc_to_taken=i;
}
}