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dalign24.c
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/*Copyrite 1995 Ward Wheeler, all rights reserved*/
/*functions to do alignments the new faster way ala Gladstein*/
/*In TBR should reroot at top ! in seperate SPR loop*/
#include "align3.h"
extern int ***best_nodes;
alignment **make_dave_align(a,ntax,nodes,l,best_aligns,values,parallel_modify)
alignment **a, **best_aligns;
int ntax, *l, **nodes,parallel_modify;
parameters *values;
{
int i,j,k,ll,value,cur_val,n,m;
int initial_length,d1,d2;
int *anc,check;
int d3,best_j;
int bufid,type,bytes,source,index,info,num_to_do,num_to_receive;
int **temp_nodes,will_be_OK,**cur_groups,ngroups2;
int ii,jj,same,kk,done;
int d1_thang, d2_thang;
alignment **a_best;
int *order,set,old_cur_val,temp,temp2;
int *dumb_sup;
alignment *temp_align,**check_buf;
int best_k,local_grain,grain_really_sent;
int found_better,smeg;
temp_align=NULL;
check=HUGE_COST;
if (values->best_order & !values->reorder) {
for (i=1;i<ntax-1;i++) {
temp_align=nw(a[0],a[i],values);
if (temp_align->score < check) {
check=temp_align->score;
best_j=i;
}
temp_align=dump_align(temp_align);
}
if (best_j != 1) {
temp_align=make_align(a[1]);
a[1]=dump_align(a[1]);
a[1]=make_align(a[best_j]);
a[best_j]=dump_align(a[best_j]);
a[best_j]=make_align(temp_align);
temp_align=dump_align(temp_align);
}
}
best_nodes=(int ***)malloc(values->keep_aligns*sizeof(int **));
assert((int) best_nodes);
for (j=0;j<values->keep_aligns;j++) {
best_nodes[j]=(int **)malloc((ntax-1)*sizeof(int *));
assert((int)best_nodes[j]);
for (i=0;i<ntax-1;i++) {
best_nodes[j][i]=(int *)malloc(2*sizeof(int));
assert((int) best_nodes[j][i]);
}
}
temp_nodes=(int **)malloc((ntax-1)*sizeof(int *));
assert((int)temp_nodes);
for (i=0;i<ntax-1;i++) {
temp_nodes[i]=(int *)malloc(2*sizeof(int));
assert((int) temp_nodes[i]);
}
anc=(int *)malloc(((2*ntax)-1)*sizeof(int));
assert((int) anc);
if (!(PARALLEL && values->jackboot)) fprintf(stderr,"Adding sequence ");
/*set so no automatic cladogram*/
values->phylo_score=0;
values->in_some=1;
/*get initial tree REMEMBER all < ntax are shifted one*/
nodes[0][0]=0;/*this should never be referenced*/
nodes[0][1]=ntax+1; /*real base ofmultiple alignment or whatever*/
nodes[1][0]=1;
nodes[1][1]=2;
if (a[ntax+1]) a[ntax+1]=dump_align(a[ntax+1]);
a[ntax+1]=nw(a[0],a[1],values); /*first node*/
anc[0]=ntax;
anc[1]=ntax+1;
anc[2]=ntax+1;
anc[ntax+1]=ntax;
anc[ntax]=ntax;
will_be_OK=1;
a_best=(alignment **)malloc((ntax-1)*sizeof(alignment *));
assert((int) a_best);
for (i=0;i<ntax-1;i++) a_best[i]=NULL;
/* and optimized nodes*/
for (i=0;i<ntax-3;i++) {/*add taxa in turn but numbers are jacked up by one*/
best_k=i+2;
if (!(PARALLEL && values->jackboot)) if (!(PARALLEL && values->jackboot)) fprintf(stderr,"%d ",i+3);
if (i==(ntax-4)) if (!(PARALLEL && values->jackboot)) fprintf(stderr,"\n");
value=HUGE_COST;
if (i==0) old_cur_val=HUGE_COST;
if (PARALLEL*parallel_modify) {
/*send all i and nodes */
pvm_initsend( PvmDataDefault );
pvm_pkint(&i,1,1);
if (values->best_order) for (ii=0;ii<ntax-1;ii++) pack_align(a[ii]);
for (j=1;j<i+2;j++) pack_align(a[ntax+j]); /*i+2 because only previous i is done*/
for (ii=0;ii<i+3;ii++) for (jj=0;jj<2;jj++) pvm_pkint(&(nodes[ii][jj]),1,1);
pvm_mcast(&(values->tids[1]),min( values->num_hosts-1,((2*i)+3)), PVM_SEND_ANODES);
num_to_receive=0;
if (values->grain_size !=1) {
local_grain=(((2*i)+3)/(values->num_hosts-1));
if (!local_grain) local_grain=1;
local_grain=min(local_grain,values->grain_size);
}
else local_grain=1;
grain_really_sent=0;
j=kk=1;
/*j is the host kk is th placement ll is the internal counter NB if grain 1 k=j
fprintf(stderr,"Local grain=%d\n",local_grain);*/
for (j=1;((num_to_receive<(values->num_hosts-1)) && ((kk+local_grain-1)<=((2*i)+3)));j++) {
pvm_initsend( PvmDataDefault );
/*pack info basics*/
pvm_pkint(&i,1,1);
/*if (values->best_order) if (i>0) for (ii=i-1;ii<ntax-1;ii++) pack_align(a[ii]);*/
pvm_pkint(&j,1,1);
pvm_pkint(&value,1,1);
pvm_pkint(&local_grain,1,1);
pvm_pkint(&kk,1,1);
/*for (smeg=0;smeg<local_grain;smeg++) {
for (ii=0;ii<i+3;ii++) for (jj=0;jj<2;jj++) temp_nodes[ii][jj]=nodes[ii][jj];
temp_nodes[i+2][0]=i+3;
temp_nodes[i+2][1]=nodes[kk/2][kk%2];
temp_nodes[kk/2][kk%2]=ntax+i+2;
for (ii=0;ii<i+3;ii++) for (jj=0;jj<2;jj++) pvm_pkint(&(temp_nodes[ii][jj]),1,1);
kk++;
}*/
pvm_send(values->tids[++num_to_receive],PVM_DAVE_BUILD);
kk+=local_grain;
/*if (!(PARALLEL && values->jackboot)) fprintf(stderr,"S%d ",num_to_receive);*/
}
/*fprintf(stderr,"End of send topos %d parts %d\n",kk-1,num_to_receive);*/
/*local_grain=1; to get straglers*/
j=kk;
/*exit(-1);*/
/*receive/send*/
while (num_to_receive>0) { /*rest as get 'em send for now--only one each no matter what the grain*/
bufid=pvm_recv(-1,PVM_DAVE_BUILD_DONE);
if (bufid) {
info=pvm_bufinfo(bufid, &bytes, &type, &source);
pvm_upkint(&index,1,1);
pvm_upkint(&cur_val,1,1);
if (cur_val<value) {value=cur_val;found_better=1;}
else found_better=0;
/*if more to do send out next*/
/*if ((kk+local_grain) > ((2*i)+3)) local_grain=((2*i)+3)-kk;*/
if ((kk + local_grain -1) > ((2*i)+3)) local_grain=( ((2*i)+3)-kk+1);
if (kk <=((2*i)+3)) {
pvm_initsend( PvmDataDefault );
/*pack info*/
pvm_pkint(&i,1,1);
/*if (values->best_order) if (i>0) for (ii=i-1;ii<ntax-1;ii++) pack_align(a[ii]);*/
pvm_pkint(&j,1,1);
pvm_pkint(&value,1,1);
pvm_pkint(&local_grain,1,1);
pvm_pkint(&kk,1,1);
/*for (smeg=0;smeg<local_grain;smeg++) {
for (ii=0;ii<i+3;ii++) for (jj=0;jj<2;jj++) temp_nodes[ii][jj]=nodes[ii][jj];
temp_nodes[i+2][0]=i+3;
temp_nodes[i+2][1]=nodes[kk/2][kk%2];
temp_nodes[kk/2][kk%2]=ntax+i+2;
for (ii=0;ii<i+3;ii++) for (jj=0;jj<2;jj++) pvm_pkint(&(temp_nodes[ii][jj]),1,1);
++kk;
}*/
pvm_send(source,PVM_DAVE_BUILD);
++num_to_receive;
++j;
kk+=local_grain;
}/*j*/
/*unpack results still only recieving one fomr each--only the best sent*/
if (found_better) {
/*value=cur_val;*/
best_j=index;
pvm_upkint(&best_k,1,1);
for (k=0;k<i+2;k++) {
if (a_best[k]) a_best[k]=dump_align(a_best[k]);
a_best[k]=unpack_align_and_score(values);
}
if (value==old_cur_val) j=HUGE_COST;
}
else pvm_freebuf(bufid);
--num_to_receive;
}/*bufid*/
}/*while*/
/*send all kill signal to dump nodes*/
pvm_initsend( PvmDataDefault );
pvm_mcast(&(values->tids[1]),min( values->num_hosts-1,((2*i)+3)), PVM_DAVE_DUMP_NODES);
}/*PARALLEL*parallel_modify*/
else {
order=(int *)malloc(ntax*sizeof(int));
assert((int)order);
for (j=1;j<=((2*i)+3);j++) {/*places to go*/
for (ii=0;ii<ntax-1;ii++) for (jj=0;jj<2;jj++) temp_nodes[ii][jj]=nodes[ii][jj];
temp_nodes[i+2][0]=i+3;
temp_nodes[i+2][1]=nodes[j/2][j%2];
temp_nodes[j/2][j%2]=ntax+i+2;
anc[i+3]=i+2+ntax;
anc[temp_nodes[i+2][1]]=i+2+ntax;
anc[i+2+ntax]=(j/2)+ntax;
if (values->groups) {
cur_groups=get_cur_groups(temp_nodes,ntax,i+4,&ngroups2);
will_be_OK=compare_groups(values->groups,cur_groups,values->ngroups,ngroups2,ntax-1,i+4-1);
for (ii=0;ii<ngroups2;ii++) free(cur_groups[ii]);
free(cur_groups);
}
if (will_be_OK) {
/*set up nodes to do and order*/
for (k=0;k<ntax;k++) order[k]=(-1);
order[0]=i+2;
num_to_do=1;
done=0;
while (!done) {
done=1;
for (k=1;k<i+3;k++) {
same=0;
for (kk=0;kk<num_to_do;kk++) if (order[kk]==k) same=1;
if (!same) {
for (kk=0;kk<num_to_do;kk++) {
if (temp_nodes[k][0]==(order[kk]+ntax)) {
order[num_to_do++]=k;
done=0;
}
else if (temp_nodes[k][1]==(order[kk]+ntax)) {
order[num_to_do++]=k;
done=0;
}
}
}
}
}
/*do_alignment*/
/*fprintf(stderr,"%d ",values->new_optimization);*/
/*could put loop in here for best adddiotn sequence*/
if (values->best_order) {
for (k=i+2;k<ntax-1;k++) {
if (k!=(i+2)) {
temp_align=make_align(a[i+2]);
a[i+2]=dump_align(a[i+2]);
a[i+2]=make_align(a[k]);
}
cur_val=all_diagnose_tree_cut_off(a,temp_nodes,ntax,i+4,values,order,num_to_do,value,a_best);
if (cur_val<value) {
value=cur_val;
best_j=j;
best_k=k;
if (value==old_cur_val) goto end_of_loop_zero;
}
if (k!=(i+2)) {
a[i+2]=dump_align(a[i+2]);
a[i+2]=make_align(temp_align);
temp_align=dump_align(temp_align);
}
/*fprintf(stderr,".");*/
}
}
else {
cur_val=all_diagnose_tree_cut_off(a,temp_nodes,ntax,i+4,values,order,num_to_do,value,a_best);
if (cur_val<value) {
value=cur_val;
best_j=j;
best_k=i+2;
if (value==old_cur_val) goto end_of_loop_zero;
}
}
}
}/*j*/
end_of_loop_zero:
;
free(order);
}/*!PARRALEL*/
/*make new nodes*/
nodes[i+2][0]=i+3; /*i+2 above because of the 1 offset when < ntax*/
d1=best_j/2;
d2=best_j%2;
nodes[i+2][1]=nodes[d1][d2];
nodes[d1][d2]=ntax+i+2;
/*get new anc and its anc*/
anc[nodes[i+2][0]]=i+2+ntax;
anc[nodes[i+2][1]]=i+2+ntax;
anc[i+2+ntax]=d1+ntax;
/*value=all_diagnose_tree_here(a,nodes,ntax,i+4,values,HUGE_COST);*/
/*copy bestnodes over for next round*/
if (values->best_order) {
if (best_k != (i+2)) {
temp_align=make_align(a[i+2]);
a[i+2]=dump_align(a[i+2]);
a[i+2]=make_align(a[best_k]);
a[best_k]=dump_align(a[best_k]);
a[best_k]=make_align(temp_align);
temp_align=dump_align(temp_align);
}
}
for (k=0;k<i+2;k++) {
if (a[k+ntax+1]) a[k+ntax+1]=dump_align(a[k+ntax+1]);
a[k+ntax+1]=a_best[k];
a_best[k]=NULL;
}
if (i==(ntax-4)) {
/*added last*/
/*if (!(PARALLEL && values->jackboot)) fprintf(stderr,"adding last\n");*/
if (best_aligns[0]) best_aligns[0]=dump_align(best_aligns[0]);
best_aligns[0]=make_align(a[nodes[0][1]]);
best_aligns[0]->score=value;
*l=1;
}
else old_cur_val=value;
}/*i loop*/
/*do_swap before freeeing*/
/*fprintf(stderr,"%d length",all_diagnose_tree_here3(a,nodes,ntax,ntax,values,HUGE_COST));*/
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 (values->new_optimization && (values->collapse==2)) {
free(best_aligns[0]->name);
dumb_sup=(int *)malloc(ntax*sizeof(int));
assert((int) dumb_sup);
for (i=0;i<ntax;i++) dumb_sup[i]=1;
best_aligns[0]->name=(char *)get_names_with_collapse(a,nodes,ntax,ntax,values,dumb_sup);
free(dumb_sup);
}
else if (values->new_optimization && (values->collapse!=2)) {
/*redo name for collapse*/
if (!values->asbr || (values->asbr && values->aquick)) check=get_collapsed_thang(best_aligns[0],nodes,ntax,check_buf,PARALLEL*parallel_modify*1,values);
}
if (values->poopsy && (!values->jackboot)) fprintf(stderr,"%s\n",best_aligns[0]->name);
for (i=0;i<ntax-1;i++) for (j=0;j<2;j++) best_nodes[0][i][j]=nodes[i][j];
if (values->asbr) {
if (values->VERBOSE && (!(PARALLEL && values->jackboot))) fprintf(stderr,"Heuristic build yielded 1 alignment at length %d\n",best_aligns[0]->score);
if (!values->tbr_first) {
temp=0;
if (values->atbr) {
temp=1;
values->atbr=0;
temp2=values->aquick;
values->aquick=1;
}
if (!values->aquick) best_aligns=do_swap_thang_align_dave(a,ntax,nodes,l,best_aligns,values,anc,1,parallel_modify);
else best_aligns=do_swap_thang_align_dave(a,ntax,nodes,l,best_aligns,values,anc,0,parallel_modify);
if (temp) {
values->atbr=1;
values->aquick=temp2;
if (!values->aquick) best_aligns=do_swap_thang_align_dave(a,ntax,nodes,l,best_aligns,values,anc,1,parallel_modify);
else best_aligns=do_swap_thang_align_dave(a,ntax,nodes,l,best_aligns,values,anc,0,parallel_modify);
}
}
else {
if (!values->aquick) best_aligns=do_swap_thang_align_dave(a,ntax,nodes,l,best_aligns,values,anc,1,parallel_modify);
else best_aligns=do_swap_thang_align_dave(a,ntax,nodes,l,best_aligns,values,anc,0,parallel_modify);
}
}
/*for (i=0;i<ntax-1;i++) {
for (j=i+1;j<ntax-1;j++) {
temp_align=nw(a[i],a[j],values);
printf("(%s %s + %d)",a[i]->name,a[j]->name,temp_align->score);
temp_align=dump_align(temp_align);
}
printf("\n");
}
fprintf(stderr,"%d length",all_diagnose_tree_here3(a,nodes,ntax,ntax,values,HUGE_COST));*/
for (i=0;i<2*ntax-1;i++) if (check_buf[i]) check_buf[i]=dump_align(check_buf[i]);
free(check_buf);
if (anc) free(anc);
for (i=0;i<ntax-1;i++) free(temp_nodes[i]);
free(temp_nodes);
for (i=0;i<ntax-1;i++) if (a_best[i]) a_best[i]=dump_align(a_best[i]);
free(a_best);
return best_aligns;
}
int all_diagnose_tree_cut_off(a,nodes,ntax,nent,values,order,num_to_do,bound,a_best)
int **nodes;
int ntax,nent;
alignment **a,**a_best;
parameters *values;
int *order, num_to_do,bound;
{
int n,d1,d2,nent_minus_one_new;
int new_opt_score,i,j;
alignment *temp_align;
alignment **backup;
int *changed,same,num_seqs;
int nodes_actual=0;
char *temp_name;
if (nent==ntax) ++values->number;
backup=(alignment **)malloc(num_to_do*sizeof(alignment *));
assert((int) backup);
for (i=0;i<num_to_do;i++) backup[i]=NULL;
changed=(int *)malloc(num_to_do*sizeof(int));
assert((int)changed);
for (i=0;i<num_to_do;i++) {
if (a[ntax+order[i]]) backup[i]=make_align(a[ntax+order[i]]);
changed[i]=0;
}
nent_minus_one_new=nent-1;
new_opt_score=0;
for (i=1;i<nent-1;i++) {
same=0;
for (j=0;j<num_to_do;j++) if (i==order[j]) same=1;
if (!same) new_opt_score+=a[ntax+i]->score;
}
temp_align=NULL;
for (i=0;i<num_to_do;i++){
n=order[i];
d1=nodes[n][0];
d2=nodes[n][1];
/*if (!(PARALLEL && values->jackboot)) fprintf(stderr,"Making %d from %d and %d\n",order[i],d1,d2);*/
/*fix for rooting more taxa*/
if (d1<ntax) d1-=1;
if (d2<ntax) d2-=1;
if (temp_align) temp_align=dump_align(temp_align);
if (values->align_cache) {
/*make names*/
if (strcmp (a[d1]->name,a[d2]->name) > 0) temp_name=other_pair_names(a[d2]->name,a[d1]->name);
else temp_name=other_pair_names(a[d1]->name,a[d2]->name);
num_seqs=1;
for (j=0;j<strlen(temp_name);j++) if (temp_name[j]=='(') ++num_seqs;
temp_align=retrieve_align_cache(temp_name,values,values->align_cache[num_seqs-2]);
free(temp_name);
}
if (!temp_align) {
temp_align = nw(a[d1],a[d2],values);
if (values->align_cache) store_align_cache(temp_align,values,values->align_cache[num_seqs-2]);
}
/*if (!(PARALLEL && values->jackboot)) fprintf(stderr,"D");*/
++nodes_actual;
if (!a[ntax+n]) same=0;
else {
same=1;
/*if misssing same*/
if ((!only_missing(a[ntax+n])) && (!only_missing(temp_align))) for (j=0;j<temp_align->length;j++) if (a[ntax+n]->s[0][j]!=temp_align->s[0][j]) {
same=0;
break;
}
}
changed[i]=(!same);
if (!same) {
if (a[ntax+n]) a[ntax+n]=dump_align(a[ntax+n]);
a[ntax+n]=temp_align;
temp_align=NULL;
new_opt_score+=a[ntax+n]->score;
if (new_opt_score>=bound) break;
}
else {
for (j=i;j<num_to_do;j++) new_opt_score+=a[ntax+order[j]]->score;
break;
}
}
if (new_opt_score < bound) for (i=0;i<nent-2;i++) {
/*if (!(PARALLEL && values->jackboot)) fprintf(stderr,"C%d",i);*/
if (a_best[i]) a_best[i]=dump_align(a_best[i]);
a_best[i]=make_align(a[i+ntax+1]);
/*if (!(PARALLEL && values->jackboot)) fprintf(stderr,"P%d",i);*/
}
/*else if ((new_opt_score==bound) && PARALLEL*parallel_modify) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr,"C%d",i);
if (a_best[i]) a_best[i]=dump_align(a_best[i]);
a_best[i]=make_align(a[i+ntax+1]);
if (!(PARALLEL && values->jackboot)) fprintf(stderr,"P%d",i);
}*/
if (temp_align) temp_align=dump_align(temp_align);
/*
if (!(PARALLEL && values->jackboot)) fprintf(stderr,"Nodes to do ");
for (i=0;i<num_to_do;i++) if (!(PARALLEL && values->jackboot)) fprintf(stderr,"%d ",order[i]);
if (!(PARALLEL && values->jackboot)) fprintf(stderr,"\n");
for (i=1;i<nent-1;i++) {
if (temp_align) temp_align=dump_align(temp_align);
d1=nodes[i][0];
d2=nodes[i][1];
if (d1<ntax) d1-=1;
if (d2<ntax) d2-=1;
temp_align=nw(a[d1],a[d2],values);
if (!(PARALLEL && values->jackboot)) fprintf(stderr,"Node[%d] %d vs. %d\n",i,a[ntax+i]->score,temp_align->score);
temp_align=dump_align(temp_align);
}*/
/*if (!(PARALLEL && values->jackboot)) fprintf(stderr,"%d/%d ",nodes_actual,num_to_do);*/
for (i=0;i<num_to_do;i++) {
if (changed[i] && backup[i]) {
a[order[i]+ntax]=dump_align(a[order[i]+ntax]);
a[order[i]+ntax]=backup[i];
backup[i]=NULL;
}
else if (backup[i]) backup[i]=dump_align(backup[i]);
}
free(backup);
free(changed);
return(new_opt_score);
}
int all_diagnose_tree_here3(a,nodes,ntax,nent,values,bound)
int **nodes;
int ntax,nent,bound;
alignment **a;
parameters *values;
{
int n,d1,d2,nent_minus_one_new=0;
char *temp_name;
int new_opt_score;
int *num_seqs,done,dont_do;
char *check_names;
int n_seqs,j;
/*need to insure that we start with nodes which connect to terminal taxa and then nodes
which have been defined - otherwise we'll be using the optimizations of
previous topology's nodes*/
/*add in a count for the first nent and nent-1 alignments and number of taxa for entering sequences with !=1 size*/
check_names=NULL;
if (nent==ntax) ++values->number;
values->all_made=(char *)malloc(((2*ntax)-1)*sizeof(char));
assert((int)values->all_made);
for (n=0;n<ntax;n++) values->all_made[n]=1;
for (n=ntax;n<(ntax+nent-1);++n) values->all_made[n]=0;
new_opt_score=0;
done=1;
while (done) {
done=0;
for (n=(nent-2);n>0;--n){ /* don't do to zero because jack up sequence number to get all rootings (as opposed to cladograms)*/
d1=nodes[n][0];
d2=nodes[n][1];
if ((values->all_made[d1]) && (values->all_made[d2]) && (!values->all_made[ntax+n])) {
values->all_made[ntax+n]=1;
/*fix for rooting more taxa*/
if (d1<ntax) d1-=1;
if (d2<ntax) d2-=1;
/*insert name checkto make sure its not there already
if (strcmp (a[d1]->name,a[d2]->name) > 0) check_names=other_pair_names(a[d2]->name,a[d1]->name);
else check_names=other_pair_names(a[d1]->name,a[d2]->name);
if ((a[ntax+n]) && (!strcmp(check_names,a[ntax+n]->name))) dont_do=1;
else */dont_do=0;
if (!dont_do) {
if (a[ntax+n]) a[ntax+n]=dump_align(a[ntax+n]);
if (values->align_cache) {
n_seqs=1;
for (j=0;j<strlen(check_names);j++) if (check_names[j]=='(') ++n_seqs;
a[ntax+n]=retrieve_align_cache(check_names,values,values->align_cache[n_seqs-2]);
free(temp_name);
}
if (!a[ntax+n]) {
a[ntax+n] = nw(a[d1],a[d2],values);
if (values->align_cache) store_align_cache(a[ntax+n],values,values->align_cache[n_seqs-2]);
}
}
done=1;
new_opt_score+=a[ntax+n]->score;
free(check_names);
if (new_opt_score>bound) goto out;
}
}
}
out:
;
free(values->all_made);
values->all_made=NULL;
/*if (!(PARALLEL && values->jackboot)) fprintf(stderr,"%u)",_memavl());*/
return(new_opt_score);
}
int all_diagnose_tree_here(a,nodes,ntax,nent,values,bound)
int **nodes;
int ntax,nent,bound;
alignment **a;
parameters *values;
{
int n,d1,d2,nent_minus_one_new=0;
char *temp_name;
int new_opt_score;
int *num_seqs,done,dont_do;
char *check_names;
int n_seqs,j;
/*need to insure that we start with nodes which connect to terminal taxa and then nodes
which have been defined - otherwise we'll be using the optimizations of
previous topology's nodes*/
/*add in a count for the first nent and nent-1 alignments and number of taxa for entering sequences with !=1 size*/
check_names=NULL;
if (nent==ntax) ++values->number;
values->all_made=(char *)malloc(((2*ntax)-1)*sizeof(char));
assert((int)values->all_made);
for (n=0;n<ntax;n++) values->all_made[n]=1;
for (n=ntax;n<(ntax+nent-1);++n) values->all_made[n]=0;
new_opt_score=0;
done=1;
while (done) {
done=0;
for (n=(nent-2);n>0;--n){ /* don't do to zero because jack up sequence number to get all rootings (as opposed to cladograms)*/
d1=nodes[n][0];
d2=nodes[n][1];
if ((values->all_made[d1]) && (values->all_made[d2]) && (!values->all_made[ntax+n])) {
values->all_made[ntax+n]=1;
/*fix for rooting more taxa*/
if (d1<ntax) d1-=1;
if (d2<ntax) d2-=1;
/*insert name checkto make sure its not there already*/
if (strcmp (a[d1]->name,a[d2]->name) > 0) check_names=other_pair_names(a[d2]->name,a[d1]->name);
else check_names=other_pair_names(a[d1]->name,a[d2]->name);
if ((a[ntax+n]) && (!strcmp(check_names,a[ntax+n]->name))) dont_do=1;
else dont_do=0;
if (!dont_do) {
if (a[ntax+n]) a[ntax+n]=dump_align(a[ntax+n]);
if (values->align_cache) {
n_seqs=1;
for (j=0;j<strlen(check_names);j++) if (check_names[j]=='(') ++n_seqs;
a[ntax+n]=retrieve_align_cache(check_names,values,values->align_cache[n_seqs-2]);
free(temp_name);
}
if (!a[ntax+n]) {
a[ntax+n] = nw(a[d1],a[d2],values);
if (values->align_cache) store_align_cache(a[ntax+n],values,values->align_cache[n_seqs-2]);
}
}
done=1;
new_opt_score+=a[ntax+n]->score;
free(check_names);
if (new_opt_score>bound) goto out;
}
}
}
out:
;
free(values->all_made);
values->all_made=NULL;
/*if (!(PARALLEL && values->jackboot)) fprintf(stderr,"%u)",_memavl());*/
return(new_opt_score);
}
alignment **do_swap_thang_align_dave(a,ntax,nodes,l_in,best_aligns,values,anc,mult,parallel_modify)
alignment **a, **best_aligns;
int ntax, *l_in, **nodes, parallel_modify;
parameters *values;
int *anc,mult;
{
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 *temp_align;
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, all_rest;
alignment **best_aligns_holder,**check_buf;
int x,y,up_node,down_node;
int int_holder,in_trees,g_test;
char *collapse_name;
int done,same,num_to_do;
int *order,*dumb_sup,temp_length,initial;
int can_move,a_group_same,second_group_same,found,match,*temp_group;
int anc_counter,rem_counter;
initial=1;
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);
}
check_buf=NULL;
collapse_name=NULL;
values->support=NULL;
/*allocations*/
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;
}
}
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;
paren_count=0;
temp_align=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++) {
/*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*parallel_modify if can*/
if (values->new_optimization) {
/*deresolves incomming tree on mult pass of swap*/
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]);
}
}
sent=received=0;
for (i=2;i<2*(ntax-1);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);
blocked[1]=0;
node_removed=anc[cur_nodes[d1][d2]];
/*redo nodes*/
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 (num_clipped<=(ntax-3)) can_move=1;
else can_move=0;
/*if (0) { */
if (values->groups && can_move) {
/*fprintf(stderr,"Checking...");*/
/*if taxon can't move--don't swap it*/
/*if all descendents of ancestor are a group AND complement of group a goup (or single) ==> no swap);
/*get groups of base tree*/
can_move=1;
cur_groups=(int **)malloc(2*sizeof(int *));
assert((int) cur_groups);
for (ii=0;ii<2;ii++) {
cur_groups[ii]=(int *)malloc(ntax*sizeof(int));
assert((int) cur_groups[ii]);
for (j=0;j<ntax;j++) cur_groups[ii][j]=0;
}
/* get group of anc*/
a_group_same=0;
recurse_groups2(hold_nodes,ntax,ntax,d1,cur_groups[0]);
match=-1;
for (k=0;k< values->ngroups;k++) {
found=1;
for (j=0;j<ntax-1;j++) if (cur_groups[0][j]!=values->groups[k][j]) {
found=0;
break;
}
if (found==1) {
a_group_same=1;
match=k;
break;
}
}
/*fprintf(stderr,"Gone through first %d(%d)...",match,a_group_same);*/
if (a_group_same) {
if (hold_nodes[d1][!d2]<ntax) can_move=0; /* if sister singleton=>can't move*/
else {
recurse_groups2(hold_nodes,ntax,ntax,hold_nodes[d1][!d2]-ntax,cur_groups[1]);
second_group_same=0;
for (k=0;k< values->ngroups;k++) {
found=1;
for (j=0;j<ntax-1;j++) if (cur_groups[1][j]!=values->groups[k][j]) {
found=0;
break;
}
if (found==1) {
second_group_same=1;
break;
}
}
if (second_group_same) can_move=0;
}
}
for (ii=0;ii<2;ii++) free(cur_groups[ii]);
free(cur_groups);
if (!can_move) fprintf(stderr,"X");
/*if (values->atbr && (num_clipped > 2)) { if more than 2 and tbr--leave reroot possibility internally REALLY ALREADY DONE IN PREVIOUS SWAP
if (!can_move) {
can_move=1;
for (j=1;j<(2*(ntax-1));j++) blocked[j]=1;
if (d2) blocked[i-1]=0;
else blocked[i+1]=0;
}
}*/
}
if (can_move) {
order=(int *)malloc(ntax*sizeof(int));
assert((int)order);
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(&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[ii]);
pvm_send(values->tids[++sent],PVM_NEW_SWAP_DAVE);
}
else {
bufid=pvm_recv(-1,PVM_NEW_SWAP_DONE_DAVE);
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;
if (values->poopsy && (!values->jackboot)) fprintf(stderr,"%s\n",best_aligns[0]->name);
/*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->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);