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util18k.c
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/*Copyrite 1995 Ward Wheeler, all rights reserved*/
/*functions to do alignments the new faster way ala Goloboff*/
#include "align3.h"
alignment **make_heur_align_new(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 score_holder;
alignment ***a_up,*temp_align,*temp_align2;
alignment *cur_align,*cur_align2;
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,***corres;
alignment **a_down;
int d1_thang, d2_thang;
if (values->groups) {
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);
a_up=(alignment ***)malloc(((2*ntax)-1)*sizeof(alignment **));
assert((int) a_up);
for (i=0;i<2*ntax-1;i++) {
a_up[i]=(alignment **)malloc(2*sizeof(alignment *));
assert((int) a_up[i]);
a_up[i][0]=NULL;
a_up[i][1]=NULL;
}
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;
}
cur_align=NULL;
cur_align2=NULL;
temp_align=NULL;
temp_align2=NULL;
if (!(PARALLEL && values->jackboot)) fprintf(stderr,"Adding sequence ");
/*set so no automatic cladogram*/
score_holder=values->phylo_score;
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;
anc[0]=ntax;
anc[1]=ntax+1;
anc[2]=ntax+1;
anc[ntax+1]=ntax;
anc[ntax]=ntax;
will_be_OK=1;
/* and optimized nodes*/
if (a[ntax+1]) a[ntax+1]=dump_align(a[ntax+1]);
if (!values->new_optimization) {
a[ntax+1]=nw(a[0],a[1],values); /*these are hand redone bit really 1-1 AND 2-1*/
initial_length=a[ntax+1]->score;
}
else {
values->in_optimize=1;
a[ntax+1]=nw(a[0],a[1],values);
initial_length=a[ntax+1]->score;
/*print_paup(a[ntax+1],values);*/
if (temp_align) temp_align=dump_align(temp_align);
temp_align=make_align(a[ntax+1]);
temp_align=new_make_ambig(temp_align,values);/*anc with gaps*/
/*get correspondance arrays*/
if (strcmp(a[0]->name,a[1]->name)>0) {
d2_thang=0;
d1_thang=1;
}
else {
d2_thang=1;
d1_thang=0;
}
if (corres[1]) { /*these numbers are because of the taxon # jack up*/
free(corres[1][0]);
free(corres[1][1]);
free(corres[1]);
}
if (corres[2]) {
free(corres[2][0]);
free(corres[2][1]);
free(corres[2]);
}
corres[1]=get_correspondances(temp_align->s[0],a[ntax+1]->s[d1_thang],temp_align->length);
corres[2]=get_correspondances(temp_align->s[0],a[ntax+1]->s[d2_thang],temp_align->length);
if (temp_align->type_weight) {
modify_corres(corres[1],temp_align);
modify_corres(corres[2],temp_align);
}
a[ntax+1]=make_ambig(a[ntax+1],values);/*anc wo gaps*/
values->in_optimize=0;
free(temp_align);
}
/*get up passes (a's are the down passes)
the uppass notation is for the up-pass which would be needed if the second array were hit
that is up pass [x][0] is the uppass needed if the addition comes between node[x] and its left [0] descendent
it is in essence the entire alignment minus node[x][0] */
/*there are no up-passes for the root node (since never used or the terminals (again never used) */
if (!values->new_optimization) {
a_up[ntax+1][0]=make_align(a[1]);
a_up[ntax+1][1]=make_align(a[0]);
}
else {
for (i=0;i<ntax-1;i++) a_down[i]=make_align(a[i]);
a_down[ntax+1]=make_align(a[ntax+1]);
}
for (i=0;i<ntax-3;i++) {/*add taxa in turn but numbers are jacked up by one*/
if (!(PARALLEL && values->jackboot)) fprintf(stderr,"%d ",i+3);
if (i==(ntax-4)) if (!(PARALLEL*values->jackboot)) fprintf(stderr,"\n");
value=HUGE_COST;
if (PARALLEL*parallel_modify) {
num_to_receive=0;
for (j=1;((num_to_receive<(values->num_hosts-1)) && (j<=((2*i)+3)));j++) {
if (values->groups) {
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;
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) {
/*send out first num_host jobs*/
d1=j/2;
d2=j%2;
d3=nodes[d1][d2];
if (d3 < ntax) d3-=1;
pvm_initsend( PvmDataDefault );
/*pack info*/
pvm_pkint(&score_holder,1,1);
pvm_pkint(&j,1,1);
pvm_pkint(&d1,1,1);
pvm_pkint(&d2,1,1);
pvm_pkint(&d3,1,1);
pvm_pkint(&i,1,1);
pack_align(a[d3]);
if (d1>0) {
if (!values->new_optimization) pack_align(a_up[d1+ntax][d2]);
else pack_align(a[d1+ntax]);
}
pvm_send(values->tids[++num_to_receive],PVM_NEW_BUILD_ADD_FUNCTION);
}
}
while (num_to_receive>0) { /*rest as get 'em send*/
bufid=pvm_recv(-1,PVM_NEW_BUILD_ALIGNMENTS_ONLY_SEND);
if (bufid) {
info=pvm_bufinfo(bufid, &bytes, &type, &source);
/*if more to do send out next*/
if (j<=((2*i)+3)) {
if (values->groups) {
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;
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) {
d1=j/2;
d2=j%2;
d3=nodes[d1][d2];
if (d3 < ntax) d3-=1;
pvm_initsend( PvmDataDefault );
/*pack info*/
pvm_pkint(&score_holder,1,1);
pvm_pkint(&j,1,1);
pvm_pkint(&d1,1,1);
pvm_pkint(&d2,1,1);
pvm_pkint(&d3,1,1);
pvm_pkint(&i,1,1);
pack_align(a[d3]);
if (d1>0) {
if (!values->new_optimization) pack_align(a_up[d1+ntax][d2]);
else pack_align(a[d1+ntax]);
}
pvm_send(source,PVM_NEW_BUILD_ADD_FUNCTION);
++num_to_receive;
}
++j;
}
/*unpack this result*/
pvm_upkint(&index,1,1);
pvm_upkint(&cur_val,1,1);
if (cur_val <value) {
/*if new value set and keep alignment (2 if last i) */
if (!values->new_optimization) {
if (cur_align) cur_align=dump_align(cur_align);
cur_align=unpack_align_and_score(values);
}
best_j=index;
value=cur_val;
}
else if (!values->new_optimization) pvm_freebuf(bufid);
--num_to_receive;
}
}
}
else {
for (j=1;j<=((2*i)+3);j++) {/*places to go*/
if (values->groups) {
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;
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) {
d1=j/2;
d2=j%2;
d3=nodes[d1][d2];
if (d3 < ntax) d3-=1;
if (!values->new_optimization) {
temp_align=nw(a[i+2],a[d3],values);/*would be i+3 but the adjustment for jack-up*/
if (d1>0) {
temp_align2=nw(temp_align,a_up[d1+ntax][d2],values);
if (score_holder>0) {
if (!compare_aligns(temp_align2,values->previous)) temp_align2->score=values->previous->score;
else {
values->phylo_score=score_holder;
cur_val=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);
}
}
else cur_val=temp_align2->score;
}
else {
if (score_holder>0) {
if (!compare_aligns(temp_align,values->previous)) temp_align->score=values->previous->score;
else {
values->phylo_score=score_holder;
cur_val=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);
}
}
else cur_val=temp_align->score;
}
}
else {
/*if (!(PARALLEL && values->jackboot)) fprintf(stderr,"(");*/
if (d1>0) { /*like interval in phylo stuff*/
values->in_optimize=1;
if (temp_align2) temp_align2=dump_align(temp_align2);
temp_align2=nw(a[d1+ntax],a[d3],values);/*would be i+3 but the adjustment for jack-up*/
values->in_optimize=0;
temp_align2=newer_make_ambig(temp_align2,values);
temp_align=nw(a[i+2],temp_align2,values);
}
else temp_align=nw(a[i+2],a[d3],values); /*if below existant root*/
cur_val=temp_align->score;
}
/*if (!(PARALLEL && values->jackboot)) fprintf(stderr,"%d",cur_val);*/
if (cur_val<value) {
value=cur_val;
best_j=j;
if (!values->new_optimization) {
if (cur_align) cur_align=dump_align(cur_align);
cur_align=make_align(temp_align);
if (cur_align2) cur_align2=dump_align(cur_align2);
if (temp_align2) cur_align2=make_align(temp_align2);
}
}
temp_align=dump_align(temp_align);
if (temp_align2) temp_align2=dump_align(temp_align2);
/*if (!(PARALLEL*values->jackboot)) fprintf(stderr,")");*/
if (value==0) break;
}
}
}
/*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;
initial_length+=value;
if (!values->new_optimization) {
/*copy the best alignment*/
if (a[i+2+ntax]) a[i+2+ntax]=dump_align(a[i+2+ntax]);
a[i+2+ntax]=make_align(cur_align);
}
if (i<ntax-4) { /*still building*/
if (!values->new_optimization) {
if (!(PARALLEL*parallel_modify)) check=all_diagnose_tree_local(a,nodes,ntax,i+4,values,i+2+ntax);
else check=all_diagnose_tree_local_parallel(a,nodes,ntax,i+4,values,i+2+ntax);
/*get up_pass alignments*/
get_up_pass2(a,nodes,ntax,values,a_up,i+4,anc);
}
else {
if (!(PARALLEL*parallel_modify)) {
check=all_diagnose_tree_local_new_opt(a_down,nodes,ntax,i+4,values,nodes[i+2][1],corres);
get_up_pass_new_opt(a,a_down,a_up,nodes,ntax,values,i+4,anc);
}
else {
check=all_diagnose_tree_local_parallel_new_opt(a_down,nodes,ntax,i+4,values,nodes[i+2][1],corres);
/*get up_pass alignments*/
get_up_pass_new_opt_parallel(a,a_down,a_up,nodes,ntax,values,i+4,anc);
}
}
}
else { /*added last*/
if (best_aligns[0]) best_aligns[0]=dump_align(best_aligns[0]);
if (!values->new_optimization) {
if (PARALLEL*parallel_modify) best_aligns[0]=make_align(cur_align);
else {
if (cur_align2) best_aligns[0]=make_align(cur_align2);
else best_aligns[0]=make_align(cur_align);
}
}
else { /*this is unnessesary really only need the names the rest is bullshit*/
if (!(PARALLEL*parallel_modify)) check=all_diagnose_tree_local_new_opt(a_down,nodes,ntax,ntax,values,nodes[i+2][1],corres);
else check=all_diagnose_tree_local_parallel_new_opt(a_down,nodes,ntax,ntax,values,nodes[i+2][1],corres);
best_aligns[0]=make_align(a_down[nodes[0][1]]);
initial_length=best_aligns[0]->score;
}
*l=1;
}
}
values->number+=(2*ntax-5);
/*if (values->new_optimization) best_aligns[0]->score=initial_length; */
/*do_swap before freeeing*/
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,a_down,PARALLEL*parallel_modify*1,values);
}
if (!(PARALLEL && values->jackboot)) if (values->asbr) fprintf(stderr,"Heuristic build yielded a single alignment at cost %d\n",best_aligns[0]->score);
if (values->asbr) {
best_aligns=do_swap_thang_align(a,ntax,nodes,l,best_aligns,values,a_up,anc,0,score_holder,parallel_modify);
if (!values->aquick) best_aligns=do_swap_thang_align(a,ntax,nodes,l,best_aligns,values,a_up,anc,1,score_holder,parallel_modify);
}
else if (!values->new_optimization) { /*filter for alignments*/
if (!(PARALLEL*parallel_modify)) check=all_diagnose_tree_local2(a,nodes,ntax,ntax,values);
else check=all_diagnose_tree_local_parallel2(a,nodes,ntax,ntax,values);
if (compare_aligns(best_aligns[0],a[nodes[0][1]])) {
if (score_holder>0) {
values->phylo_score=score_holder;
a[nodes[0][1]]->score=cladogram(a[nodes[0][1]],values);
values->phylo_score=0;
}
if (a[nodes[0][1]]->score < best_aligns[0]->score) {
if (!(PARALLEL && values->jackboot)) fprintf(stderr," Filtering Alignment 0 => New Cost %d\n",a[nodes[0][1]]->score);
if (best_aligns[0]) best_aligns[0]=dump_align(best_aligns[0]);
best_aligns[0]=make_align(a[nodes[0][1]]);
}
}
/*at any rate fix name so matches order for OPTALI too*/
free(best_aligns[0]->name);
best_aligns[0]->name=(char *)malloc((1+strlen(a[nodes[0][1]]->name))*sizeof(char));
assert((int) best_aligns[0]->name);
strcpy(best_aligns[0]->name,a[nodes[0][1]]->name);
values->number+=((ntax-1)/2);
}
if (anc) free(anc);
if (a_up) {
for (i=0;i<2*ntax-1;i++) {
if (a_up[i][0]) a_up[i][0]=dump_align(a_up[i][0]);
if (a_up[i][1]) a_up[i][1]=dump_align(a_up[i][1]);
free(a_up[i]);
}
free(a_up);
}
if (temp_align) temp_align=dump_align(temp_align);
if (temp_align2) temp_align2=dump_align(temp_align2);
if (cur_align) cur_align=dump_align(cur_align);
if (cur_align2) cur_align2=dump_align(cur_align2);
if (values->groups) {
for (i=0;i<ntax-1;i++) free(temp_nodes[i]);
free(temp_nodes);
}
if (values->new_optimization) {
for (i=0;i<2*ntax-1;i++) if (a_down[i]) a_down[i]=dump_align(a_down[i]);
free(a_down);
for (i=0;i<2*ntax;i++) {
if (corres[i]) {
if (corres[i][0]) free(corres[i][0]);
if (corres[i][1]) free(corres[i][1]);
free(corres[i]);
}
}
free(corres);
}
values->phylo_score=score_holder;
values->in_some=0; /*return initial length ?thang for new opt filter for names???*/
return best_aligns;
}
void get_up_pass(a,nodes,ntax,values,a_up,nent,anc)
alignment **a,***a_up;
int **nodes,ntax,nent,*anc;
parameters *values;
{
int i,j,found_one,d1,d2;
int branch;
for (i=1;i<nent-1;i++) {
if (a_up[i+ntax][0]) a_up[i+ntax][0]=dump_align(a_up[i+ntax][0]);
if (a_up[i+ntax][1]) a_up[i+ntax][1]=dump_align(a_up[i+ntax][1]);
}
/*get the first two*/
d1=nodes[nodes[0][1]-ntax][1];
d2=nodes[nodes[0][1]-ntax][0];
/*if terminal*/
if (d1<ntax) d1-=1;
if (d2<ntax) d2-=1;
a_up[nodes[0][1]][0]=make_align(a[d1]);
a_up[nodes[0][1]][1]=make_align(a[d2]);
found_one=1;
while (found_one) {
found_one=0;
for (i=1;i<nent-1;i++) if ((!a_up[i+ntax][0]) && (a_up[anc[i+ntax]][0])){
found_one=1;
d1=nodes[i][0];
d2=nodes[i][1];
if (nodes[anc[i+ntax]-ntax][0]==(i+ntax)) branch=0;
else branch=1;
if (d1<ntax) d1-=1;
if (d2<ntax) d2-=1;
a_up[i+ntax][0]=nw(a_up[anc[i+ntax]][branch],a[d2],values);
a_up[i+ntax][1]=nw(a_up[anc[i+ntax]][branch],a[d1],values);
}
}
}
void get_up_pass2(a,nodes,ntax,values,a_up,nent,anc)
alignment **a,***a_up;
int **nodes,ntax,nent,*anc;
parameters *values;
{
int i,j,k,l;
int n_seqs,length;
char **names, **bases;
int found,seq_counter,*all_gaps;
int new_length,l_counter,d1;
alignment *an,*auij;
/*deallocate 'em all*/
for (i=1;i<nent-1;i++) {
if (a_up[i+ntax][0]) a_up[i+ntax][0]=dump_align(a_up[i+ntax][0]);
if (a_up[i+ntax][1]) a_up[i+ntax][1]=dump_align(a_up[i+ntax][1]);
}
/*BASIC IDEA => a_up[i][j]=a[nodes[0][1]]-a[nodes[i-ntax][j]]*/
an=a[nodes[0][1]];
/*alloacte holders*/
n_seqs=an->n_seqs;
length=an->length;
names=(char **)malloc(n_seqs*sizeof(char *));
assert((int)names);
bases=(char **)malloc((n_seqs+an->type_weight)*sizeof(char *));
assert((int)bases);
for (i=0;i<(n_seqs+an->type_weight);i++) {
if (i<n_seqs) {
names[i]=(char *)malloc(100*sizeof(char));
assert((int)names[i]);
}
bases[i]=(char *)malloc((1+length)*sizeof(char));
assert((int)bases[i]);
}
all_gaps=(int *)malloc(length*sizeof(int));
assert((int)all_gaps);
/*doit*/
for (i=ntax+1;i<ntax+nent-1;i++) for (j=0;j<2;j++){
d1=nodes[i-ntax][j];
if (d1 < ntax) d1-=1;
seq_counter=0;
for (k=0;k<n_seqs;k++) {
found=0;
for (l=0;l<a[d1]->n_seqs;l++) if (!strcmp(an->taxon_name[k],a[d1]->taxon_name[l])) found=1;
if (!found) { /*want these*/
strcpy(names[seq_counter],an->taxon_name[k]);
strcpy(bases[seq_counter],an->s[k]);
++seq_counter;
}
}/*k*/
if (an->type_weight) {
strcpy(bases[seq_counter],an->s[an->n_seqs]);/*type_weight stuff*/
}
/*check seqs copied are correct in number*/
if (seq_counter==(n_seqs-a[d1]->n_seqs)) { /*else in sbr/tbr non-needed up-passes*/
/*scan for all gaps in remainder*/
for (k=0;k<length;k++) {
all_gaps[k]=1;
for (l=0;l<seq_counter+an->type_weight;l++) {
if (bases[l][k]!='-') all_gaps[k]=0;
if ((l==seq_counter) && an->type_weight && (an->s[l][k]!=0)) all_gaps[k]=0;
}
}
new_length=0;
for (k=0;k<length;k++) if (!all_gaps[k]) ++new_length;
/*allocate and copy to a_up[i][j]*/
a_up[i][j]=NULL;
a_up[i][j]=(alignment *)malloc(sizeof(alignment));
assert((int)a_up[i][j]);
auij=a_up[i][j];
auij->n_seqs=seq_counter;
auij->score=0;
auij->length=new_length;
auij->type_weight=an->type_weight;
auij->name=(char *)malloc(8*sizeof(char));
assert((int) auij->name);
auij->name[0]='U';
auij->name[1]='p';
auij->name[2]='-';
auij->name[3]='P';
auij->name[4]='a';
auij->name[5]='s';
auij->name[6]='s';
auij->name[7]='\0';
auij->s=(char **)malloc((auij->n_seqs+auij->type_weight)*sizeof(char *));
assert((int)auij->s);
for (k=0;k<(auij->n_seqs+auij->type_weight);k++) {
auij->s[k]=(char *)malloc((auij->length+1)*sizeof(char));
assert((int)auij->s[k]);
l_counter=0;
for (l=0;l<length;l++) {
if (!all_gaps[l]) auij->s[k][l_counter++]=bases[k][l];
else if (auij->type_weight && (k==auij->n_seqs)) {
if (bases[k][l]>60) auij->s[k][l_counter-1]=bases[k][l];
}
}
auij->s[k][new_length]='\0';
}
auij->taxon_name=(char **)malloc((auij->n_seqs)*sizeof(char *));
assert((int)auij->taxon_name);
for (k=0;k<auij->n_seqs;k++) {
auij->taxon_name[k]=(char *)malloc((strlen(names[k])+1)*sizeof(char));
assert((int)auij->taxon_name[k]);
auij->taxon_name[k]=(char *)strcpy(auij->taxon_name[k],names[k]);
}
/*print_alignment(auij);
printf("\n");*/
}
}
/*freeing*/
for (i=0;i<n_seqs+an->type_weight;i++) {
if (i<n_seqs) free(names[i]);
free(bases[i]);
}
free(names);
free(bases);
free(all_gaps);
}
void get_up_pass3(a,nodes,ntax,values,a_up,nent,anc,desc)
alignment **a,***a_up;
int **nodes,ntax,nent,*anc,*desc;
parameters *values;
{
int i,j,k,l;
int n_seqs,length;
char **names, **bases;
int found,seq_counter,*all_gaps;
int new_length,l_counter,d1;
/*deallocate 'em all*/
for (i=1;i<nent-1;i++) {
if (a_up[i+ntax][0]) a_up[i+ntax][0]=dump_align(a_up[i+ntax][0]);
if (a_up[i+ntax][1]) a_up[i+ntax][1]=dump_align(a_up[i+ntax][1]);
}
/*BASIC IDEA => a_up[i][j]=a[nodes[0][1]]-a[nodes[i-ntax][j]]*/
/*alloacte holders*/
n_seqs=a[nodes[0][1]]->n_seqs;
length=a[nodes[0][1]]->length;
names=(char **)malloc(n_seqs*sizeof(char *));
assert((int)names);
bases=(char **)malloc(n_seqs*sizeof(char *));
assert((int)bases);
for (i=0;i<n_seqs;i++) {
names[i]=(char *)malloc(100*sizeof(char));
assert((int)names[i]);
bases[i]=(char *)malloc((1+length)*sizeof(char));
assert((int)bases[i]);
}
all_gaps=(int *)malloc(length*sizeof(int));
assert((int)all_gaps);
/*doit*/
for (i=ntax+1;i<ntax+nent-1;i++) for (j=0;j<2;j++){
d1=nodes[i-ntax][j];
if (d1 < ntax) d1-=1;
seq_counter=0;
for (k=0;k<n_seqs;k++) {
found=0;
for (l=0;l<a[d1]->n_seqs;l++) if (!strcmp(a[nodes[0][1]]->taxon_name[k],a[d1]->taxon_name[l])) found=1;
if (!found) { /*want these*/
strcpy(names[seq_counter],a[nodes[0][1]]->taxon_name[k]);
strcpy(bases[seq_counter],a[nodes[0][1]]->s[k]);
++seq_counter;
}
}/*k*/
/*check seqs copied are correct in number*/
if (seq_counter==(n_seqs-a[d1]->n_seqs)) { /*else in sbr/tbr non-needed up-passes*/
/*scan for all gaps in remainder*/
for (k=0;k<length;k++) {
all_gaps[k]=1;
for (l=0;l<seq_counter;l++) if (bases[l][k]!='-') all_gaps[k]=0;
}
new_length=0;
for (k=0;k<length;k++) if (!all_gaps[k]) ++new_length;
/*allocate and copy to a_up[i][j]*/
a_up[i][j]=(alignment *)malloc(sizeof(alignment));
assert((int)a_up[i][j]);
a_up[i][j]->n_seqs=seq_counter;
a_up[i][j]->score=0;
a_up[i][j]->length=new_length;
a_up[i][j]->type_weight=0;
a_up[i][j]->name=(char *)malloc(8*sizeof(char));
assert((int)a_up[i][j]->name);
a_up[i][j]->name[0]='U';
a_up[i][j]->name[1]='p';
a_up[i][j]->name[2]='-';
a_up[i][j]->name[3]='P';
a_up[i][j]->name[4]='a';
a_up[i][j]->name[5]='s';
a_up[i][j]->name[6]='s';
a_up[i][j]->name[7]='\0';
a_up[i][j]->s=(char **)malloc((a_up[i][j]->n_seqs+a_up[i][j]->type_weight)*sizeof(char *));
assert((int)a_up[i][j]->s);
for (k=0;k<(a_up[i][j]->n_seqs+a_up[i][j]->type_weight);k++) {
a_up[i][j]->s[k]=(char *)malloc((a_up[i][j]->length+1)*sizeof(char));
assert((int)a_up[i][j]->s[k]);
l_counter=0;
for (l=0;l<length;l++) if (!all_gaps[l]) a_up[i][j]->s[k][l_counter++]=bases[k][l];
a_up[i][j]->s[k][new_length]='\0';
}
a_up[i][j]->taxon_name=(char **)malloc((a_up[i][j]->n_seqs)*sizeof(char *));
assert((int)a_up[i][j]->taxon_name);
for (k=0;k<a_up[i][j]->n_seqs;k++) {
a_up[i][j]->taxon_name[k]=(char *)malloc((strlen(names[k])+1)*sizeof(char));
assert((int)a_up[i][j]->taxon_name[k]);
a_up[i][j]->taxon_name[k]=(char *)strcpy(a_up[i][j]->taxon_name[k],names[k]);
}
/*print_alignment(a_up[i][j]);
printf("\n");*/
}
}
/*freeing*/
for (i=0;i<n_seqs;i++) {
free(names[i]);
free(bases[i]);
}
free(names);
free(bases);
free(all_gaps);
/*if (!(PARALLEL*values->jackboot)) fprintf(stderr,"Done up_pass\n");exit(-1);*/
}
int all_diagnose_tree_local(a,nodes,ntaxa,nent,values,node_made)
int **nodes,node_made;
int ntaxa,nent;
alignment **a;
parameters *values;
{
int n,d1,d2,nent_minus_one_new=0;
char *temp_name;
int new_opt_score;
int *num_seqs,found_one;
num_seqs=(int *)malloc((ntaxa+ntaxa-1)*sizeof(int));
assert((int)num_seqs);
values->in_some=1;
values->all_made=(char *)malloc(((2*ntaxa)-1)*sizeof(char));
assert((int)values->all_made);
for (n=0;n<ntaxa;n++) values->all_made[n]=1;
for (n=ntaxa;n<(ntaxa+nent-1);++n) values->all_made[n]=0;
/*make sure the in-some check works for multiple input alignments*/
if (values->number_of_input_alignments<1) nent_minus_one_new=nent-1;
else if ((!values->new_optimization)) nent_minus_one_new=nent-1;
else for (n=0;n<=(nent-1);n++) nent_minus_one_new+=a[n]->n_seqs;
pre_diagnose_align(a,nodes,ntaxa,nent,values,num_seqs);
values->all_made[node_made]=1;
found_one=1;
while (found_one) {
found_one=0;
for (n=0;n<nent_minus_one_new;n++) if (values->all_made[n+ntaxa] && ((!values->all_made[nodes[n][0]]) || (!values->all_made[nodes[n][1]]))) {
found_one=1;
values->all_made[nodes[n][0]]=1;
values->all_made[nodes[n][1]]=1;
}
}
/*if (!(PARALLEL*values->jackboot)) fprintf(stderr,"%u-",_memavl());*/
found_one=1;
while (found_one) {
found_one=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[ntaxa+n])) {
found_one=1;
values->all_made[ntaxa+n]=1;
/*fix for rooting more taxa*/
if (d1<ntaxa) d1-=1;
if (d2<ntaxa) d2-=1;
/*avoid unnesesary trees*/
if ((a[d1]->n_seqs+a[d2]->n_seqs)<(nent_minus_one_new)) {
if (a[ntaxa+n]) a[ntaxa+n]=dump_align(a[ntaxa+n]);
a[ntaxa+n] = nw(a[d1],a[d2],values);
/*++temp_done;*/
if (values->align_cache) store_align_cache(a[ntaxa+n],values,values->align_cache[a[ntaxa+n]->n_seqs-2]);
if (values->in_bandb_loop && (a[ntaxa+n]->score>values->current_bound)) goto second_end;
}
else {
if (a[ntaxa+n]) a[ntaxa+n]=dump_align(a[ntaxa+n]);
a[ntaxa+n] = nw(a[d1],a[d2],values);
/*++temp_done;*/
if (values->align_cache) store_align_cache(a[ntaxa+n],values,values->align_cache[a[ntaxa+n]->n_seqs-2]);
}
}
}
}
free(num_seqs);
free(values->all_made);
values->all_made=NULL;
/*if (!(PARALLEL*values->jackboot)) fprintf(stderr,"%u)",_memavl());*/
values->in_some=0;
return(a[nodes[0][1]]->score);
/*if early exceed bound*/
second_end:
free(num_seqs);
free(values->all_made);
values->in_some=0;
values->all_made=NULL;
return HUGE_COST;
}
int all_diagnose_tree_local_parallel2(a,nodes,ntaxa,nent,values)
int **nodes;
int ntaxa,nent;
alignment **a;
parameters *values;
{
int n,d1,d2,nent_minus_one_new=0;
char *temp_name;
int new_opt_score;
int *num_seqs,found_one;
int sent,received,score_holder,node_to_be_sent;
int node_received,bufid,info,source,tag,bytes,type;
int ii;
num_seqs=(int *)malloc((ntaxa+ntaxa-1)*sizeof(int));
assert((int)num_seqs);
values->in_some=1;
values->all_made=(char *)malloc(((2*ntaxa)-1)*sizeof(char));
assert((int)values->all_made);
for (n=0;n<ntaxa;n++) values->all_made[n]=1;
for (n=ntaxa;n<(ntaxa+nent-1);++n) values->all_made[n]=0;
/*make sure the in-some check works for multiple input alignments*/
if (values->number_of_input_alignments<1) nent_minus_one_new=nent-1;
else if ((!values->new_optimization)) nent_minus_one_new=nent-1;
else for (n=0;n<=(nent-1);n++) nent_minus_one_new+=a[n]->n_seqs;
/*mark stuff that's already done*/
pre_diagnose_align(a,nodes,ntaxa,nent,values,num_seqs);
score_holder=0;
found_one=1;
while (found_one) {
found_one=0;
sent=received=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[ntaxa+n])) {
found_one=1;
/*fix for rooting more taxa*/
if (d1<ntaxa) d1-=1;
if (d2<ntaxa) d2-=1;
node_to_be_sent=ntaxa+n;
if (sent < (values->num_hosts-1)) {
pvm_initsend( PvmDataDefault );
pvm_pkint(&score_holder,1,1);
pvm_pkint(&node_to_be_sent,1,1);
pack_align(a[d1]);
pack_align(a[d2]);
pvm_send(values->tids[++sent],PVM_PARALLEL_NW);
}
else {
bufid=pvm_recv(-1,PVM_PARALLEL_NW_DONE);
if (bufid) {
info=pvm_bufinfo(bufid, &bytes, &type, &source);
pvm_upkint(&node_received,1,1);
if (a[node_received]) a[node_received]=dump_align(a[node_received]);
a[node_received]=unpack_align_and_score(values);
values->all_made[node_received]=1;
++received;
}
pvm_initsend( PvmDataDefault );
pvm_pkint(&score_holder,1,1);
pvm_pkint(&node_to_be_sent,1,1);
pack_align(a[d1]);
pack_align(a[d2]);
pvm_send(source,PVM_PARALLEL_NW);
++sent;
}
}
}
/*receive the remainder*/
/*while (received<sent) {*/
for (ii=received;ii<sent;ii++) {
bufid=pvm_recv(-1,PVM_PARALLEL_NW_DONE);
if (bufid) {
info=pvm_bufinfo(bufid, &bytes, &type, &source);
pvm_upkint(&node_received,1,1);
if (a[node_received]) a[node_received]=dump_align(a[node_received]);
a[node_received]=unpack_align_and_score(values);
values->all_made[node_received]=1;
/*++received;*/
}
}
}
free(num_seqs);
free(values->all_made);
values->all_made=NULL;
/*if (!(PARALLEL*values->jackboot)) fprintf(stderr,"%u)",_memavl());*/
values->in_some=0;
return(a[nodes[0][1]]->score);
/*if early exceed bound*/
second_end:
free(num_seqs);
free(values->all_made);
values->in_some=0;
values->all_made=NULL;
return HUGE_COST;
}
int all_diagnose_tree_local_parallel(a,nodes,ntaxa,nent,values,node_made)
int **nodes,node_made;
int ntaxa,nent;
alignment **a;
parameters *values;
{
int n,d1,d2,nent_minus_one_new=0;
char *temp_name;
int new_opt_score;
int *num_seqs,found_one;
int sent,received,score_holder,node_to_be_sent;
int node_received,bufid,info,source,tag,bytes,type;
int ii;
num_seqs=(int *)malloc((ntaxa+ntaxa-1)*sizeof(int));
assert((int)num_seqs);
values->in_some=1;
values->all_made=(char *)malloc(((2*ntaxa)-1)*sizeof(char));
assert((int)values->all_made);
for (n=0;n<ntaxa;n++) values->all_made[n]=1;
for (n=ntaxa;n<(ntaxa+nent-1);++n) values->all_made[n]=0;
/*make sure the in-some check works for multiple input alignments*/
if (values->number_of_input_alignments<1) nent_minus_one_new=nent-1;
else if ((!values->new_optimization)) nent_minus_one_new=nent-1;
else for (n=0;n<=(nent-1);n++) nent_minus_one_new+=a[n]->n_seqs;
/*mark stuff that's already done*/
pre_diagnose_align(a,nodes,ntaxa,nent,values,num_seqs);
values->all_made[node_made]=1;
found_one=1;
while (found_one) {
found_one=0;
for (n=0;n<nent_minus_one_new;n++) if (values->all_made[n+ntaxa] && ((!values->all_made[nodes[n][0]]) || (!values->all_made[nodes[n][1]]))) {
found_one=1;
values->all_made[nodes[n][0]]=1;
values->all_made[nodes[n][1]]=1;
}
}
score_holder=0;
found_one=1;
while (found_one) {
found_one=0;
sent=received=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[ntaxa+n])) {
found_one=1;
/*fix for rooting more taxa*/
if (d1<ntaxa) d1-=1;
if (d2<ntaxa) d2-=1;
node_to_be_sent=ntaxa+n;
if (sent < (values->num_hosts-1)) {
pvm_initsend( PvmDataDefault );
pvm_pkint(&score_holder,1,1);
pvm_pkint(&node_to_be_sent,1,1);
pack_align(a[d1]);
pack_align(a[d2]);
pvm_send(values->tids[++sent],PVM_PARALLEL_NW);
}
else {
bufid=pvm_recv(-1,PVM_PARALLEL_NW_DONE);
if (bufid) {
info=pvm_bufinfo(bufid, &bytes, &type, &source);
pvm_upkint(&node_received,1,1);
if (a[node_received]) a[node_received]=dump_align(a[node_received]);
a[node_received]=unpack_align_and_score(values);
values->all_made[node_received]=1;
++received;
}
pvm_initsend( PvmDataDefault );
pvm_pkint(&score_holder,1,1);
pvm_pkint(&node_to_be_sent,1,1);
pack_align(a[d1]);
pack_align(a[d2]);
pvm_send(source,PVM_PARALLEL_NW);
++sent;
}
}
}
/*receive the remainder*/
/*while (received<sent) {*/
for (ii=received;ii<sent;ii++) {
bufid=pvm_recv(-1,PVM_PARALLEL_NW_DONE);
if (bufid) {
info=pvm_bufinfo(bufid, &bytes, &type, &source);
pvm_upkint(&node_received,1,1);
if (a[node_received]) a[node_received]=dump_align(a[node_received]);
a[node_received]=unpack_align_and_score(values);
values->all_made[node_received]=1;
/*++received;*/
}
}
}
free(num_seqs);
free(values->all_made);
values->all_made=NULL;
/*if (!(PARALLEL*values->jackboot)) fprintf(stderr,"%u)",_memavl());*/
values->in_some=0;