/* Standard option - calculate the probability, the matrix of
* expected information and the diagonal values of the variance
* Dump these to disk and calculate the determinant of the
* expectation matrix.*/
void standard(struct treenode *node_p,FILE *file_p,unsigned int e){
#include "variables.h"
int a,b;
/* Make a copy of the tree, fill and calculate the likelihoods*/
tree2=treecopy(node_p,0);
filltree(node_p,tree2,0);
if(sample_file_p!=NULL)
fprintf(sample_file_p,"#Points 1\n\n");
/* We aren't altering the rate, so factor is 1*/
factor=1.0;
factor_flag=0;
det=find_information(node_p,tree2,e,factor_flag,factor);
/* Print the required output - may be more than one value*/
b=1;
if(NOTMODE(DETINDIV) && ISMODE(INDIVIDUAL))
b=individual;
for(a=0;a<b;a++)
fprintf(file_p,"%s = %1.11E\n",outstring,det[a]);
if(ISMODE(HKY) && NOTMODE(NOKAPPA) && NOTMODE(PERCENTILE))
fprintf(file_p,"Information about Kappa = %1.11E\n",det[b]);
free(det);
}
static void dopush(Dataptr matrix, Treestack *sp, const Branch *const barray, const long root)
/* push tree in barray (of root root) on to stack *sp */
{
lvb_assert(sp->next <= sp->size);
if (sp->next == sp->size) upsize(matrix, sp);
treecopy(matrix, sp->stack[sp->next].tree, barray);
sp->stack[sp->next].root = root;
sp->next++;
} /* end dopush() */
static int
callinstr(Node **np, NodeList **init, int wr, int skip)
{
Node *f, *b, *n;
Type *t;
int class, hascalls;
n = *np;
//print("callinstr for %+N [ %O ] etype=%E class=%d\n",
// n, n->op, n->type ? n->type->etype : -1, n->class);
if(skip || n->type == T || n->type->etype >= TIDEAL)
return 0;
t = n->type;
if(isartificial(n))
return 0;
b = basenod(n);
// it skips e.g. stores to ... parameter array
if(isartificial(b))
return 0;
class = b->class;
// BUG: we _may_ want to instrument PAUTO sometimes
// e.g. if we've got a local variable/method receiver
// that has got a pointer inside. Whether it points to
// the heap or not is impossible to know at compile time
if((class&PHEAP) || class == PPARAMREF || class == PEXTERN
|| b->op == OINDEX || b->op == ODOTPTR || b->op == OIND || b->op == OXDOT) {
hascalls = 0;
foreach(n, hascallspred, &hascalls);
if(hascalls) {
n = detachexpr(n, init);
*np = n;
}
n = treecopy(n);
makeaddable(n);
if(t->etype == TSTRUCT || isfixedarray(t)) {
f = mkcall(wr ? "racewriterange" : "racereadrange", T, init, uintptraddr(n),
nodintconst(t->width));
} else
f = mkcall(wr ? "racewrite" : "raceread", T, init, uintptraddr(n));
*init = list(*init, f);
return 1;
}
return 0;
}
long treestack_pop(Dataptr matrix, Branch *barray, long *root, Treestack *sp)
{
long val; /* return value */
if (sp->next >= 1){
sp->next--;
treecopy(matrix, barray, sp->stack[sp->next].tree);
*root = sp->stack[sp->next].root;
val = 1;
}
else{
val = 0;
}
return val;
} /* end treestack_pop() */
long treestack_print(Dataptr matrix, Treestack *sp, FILE *const outfp, Lvb_bool onerandom)
{
const long d_obj1 = 0L; /* 1st obj. for output trees */
long root; /* root of current tree */
long i; /* loop counter */
long lower; /* lowest index of trees to print */
long upper; /* 1 + upper index of trees to print */
Branch *barray; /* current unpacked tree */
/* "local" dynamic heap memory */
barray = treealloc(matrix);
if (onerandom == LVB_TRUE) /* choose one random tree to print */
{
lower = randpint(sp->next - 1);
upper = lower + 1;
} else {
lower = 0;
upper = sp->next;
}
for (i = lower; i < upper; i++) {
treecopy(matrix, barray, sp->stack[i].tree);
if (sp->stack[i].root != d_obj1) lvb_reroot(barray, sp->stack[i].root, d_obj1);
root = d_obj1;
lvb_treeprint(matrix, outfp, barray, root);
}
if (fflush(outfp) != 0)
crash("file write error when writing best trees");
/* deallocate "local" dynamic heap memory */
free(barray);
return upper - lower; /* number of trees printed */
} /* end treestack_print() */
/* Routine to vary the length of all branches by the same factor
* and dump the expected information to disk. Since we are altering
* the rate of change, we need to include a factor in all the information
* calculations*/
void growtree(struct treenode *node_p,FILE *file_p,unsigned int e){
#include "variables.h"
int steps,a,b,c;
double f_min,f_max,f;
struct treenode *tree;
/* Code to get the factors from the users*/
printf("Altering length of all branches by same factor\n\n");
printf("Please enter min. factor, max factor and number of points:\n");
do{
printf("\tmin. factor:");
scanf("%lf",&f_min);
}while(f_min<=0);
do{
printf("\tmax. factor:");
scanf("%lf",&f_max);
}while(f_min>=f_max);
do{
printf("\tnumber of points:");
scanf("%d",&steps);
}while(steps<=0);
/* Dump text to file explaining what we are about to do*/
fprintf(file_p,"#Results from Varying length of all branches by factor\n");
fprintf(file_p,"#Factor\t\t\t%s\n",outstring);
if(ISMODE(MATRICES))
fprintf(matrix_file_p,"#Matrices from Varying length of all branches by factor\n");
if(sample_file_p!=NULL){
fprintf(sample_file_p,"#Points %d\n",steps);
fprintf(sample_file_p,"#Samples from varying length of all branches by factor\n");
}
if(ISMODE(PROBS))
fprintf(prob_file_p,"#Probabilities from varying length of all branches by factor\n");
/* Start main loop*/
/* Make two copies of the tree*/
tree2=treecopy(node_p,0);
tree=treecopy(node_p,0);
/* Calculate what factor we need to include in the calculations*/
for(c=0;c<(steps);c++){
if(steps==1) /* Prevent divide by zero if only one step*/
f=f_min;
else
f=f_min+c*(f_max-f_min)/(steps-1);
factor=f;
factor_flag=-1; /* Flag = -1 means that we want to include the
* factor on all branches*/
/* Add all the information to one copy from the original tree*/
filltree(node_p,tree,0);
/* Change all the length in the tree to the scaled version
* The array branch[] currently points to those of 'tree'*/
for(b=0;b<branches;b++){
branch[b]->length[0]=branch[b]->length[0]*f;
a=findnode(branch[b]->node[0],branch[b]);
(branch[b]->node[0])->length[a]=branch[b]->length[0];
}
/* Make copy of the tree with scaled branches*/
filltree(tree,tree2,0);
/* Branch[] now points to those in tree2
* Make leaves point to those on tree*/
leaves=0;
doleaf(tree,0);
printf("Doing factor %E\n",f);
/* If we've been asked to print out the intermediate trees, then
* dump them to all the open files*/
if(ISMODE(TREES))
print_tree(tree,file_p,0);
fprintf(file_p,"%E\n",f);
if(ISMODE(MATRICES)){
fprintf(matrix_file_p,"\n#Factor %E\n",f);
if(ISMODE(TREES))
print_tree(tree,matrix_file_p,0);
}
if(ISMODE(VARIANCE)){
fprintf(variance_file_p,"\n#Factor %E\n",f);
if(ISMODE(TREES))
print_tree(tree,variance_file_p,0);
}
if(sample_file_p!=NULL){
fprintf(sample_file_p,"\n#Factor %E\n",f);
if(ISMODE(TREES))
print_tree(tree,sample_file_p,0);
}
if(ISMODE(PROBS)){
fprintf(prob_file_p,"\n#Factor %E\n",f);
if(ISMODE(TREES))
print_tree(tree,prob_file_p,0);
}
det=find_information(tree,tree2,e,factor_flag,factor);
/* Possible may want to print out more than one result*/
b=1;
if(ISMODE(INDIVIDUAL))
b=individual;
if(ISMODE(INDIVIDUAL)){
if(ISMODE(DETINDIV)){
fprintf(file_p,"\t\t\t%E\tD(",det[0]);
for(a=0;a<b-1;a++)
fprintf(file_p,"%d,",interesting_branches[a]);
fprintf(file_p,"%d)\n",interesting_branches[a]);
}else
for(a=0;a<b;a++)
fprintf(file_p,"\t\t\t%E\t%d\n",det[a],interesting_branches[a]);
}else
fprintf(file_p,"\t\t\t%E\tD\n",det[0]);
if(ISMODE(HKY) && NOTMODE(NOKAPPA) && NOTMODE(PERCENTILE))
fprintf(file_p,"\t\t\t%E\tKappa\n",det[b]);
free(det);
}
}
/* Routine to slid one branch of a node along the a branch
* The moving node is assumed to be simple!*/
void greasebranch(struct treenode *node_p,FILE *file_p,unsigned int e){
#include "variables.h"
int steps,a,b,c;
int slippe,to,from,to_root,to_false_root;
int sp_case;
double f_min,f_max,f,l;
extern int root;
struct treenode *movingnode,*node_c;
struct treenode *tree;
/* Make two copies of the tree*/
tree2=treecopy(node_p,0);
tree=treecopy(node_p,0);
filltree(node_p,tree,0);
/* Print out the tree branches and respective numbers*/
printf("\n");
for(a=0;a<branches;a++)
printf("Branch %d goes from %s to %s\n",a
,(branch[a]->node[0])->name,branch[a]->name);
/* Get the necessary parameters from the user*/
do{
printf("\nWhich branch would you like to move?");
scanf("%d",&slippe);
}while(slippe<0 || slippe>branches);
do{
printf("\nWhich branch would you like to move branch %d along(towards)?"
,slippe);
scanf("%d",&to);
printf("\nWhich branch would you like to move branch %d along(away)?"
,slippe);
scanf("%d",&from);
}while(to<0 || to>branches || from<0 || from>branches);
/* Out of the three parameters given, two of them must point
* the common node.*/
movingnode=(branch[to]->node[0]==branch[from]->node[0])
?branch[to]->node[0]:branch[slippe]->node[0];
/* Find which branch in the common node points to each of the
* parameter branches.*/
from=findnode(movingnode,branch[from]);
to=findnode(movingnode,branch[to]);
slippe=findnode(movingnode,branch[slippe]);
/* Get the amount of variation from the user*/
printf("Sliding branch leading to %s\n\n",branch[slippe]->name);
printf("Please enter min. & max. distance to move and number of points:\n");
do{
printf("\tmin. distance:");
scanf("%lf",&f_min);
}while(f_min<=-movingnode->length[from] || f_min>=movingnode->length[to]);
do{
printf("\tmax. distance:");
scanf("%lf",&f_max);
}while(f_min>=f_max || f_max>=movingnode->length[to]);
do{
printf("\tnumber of points:");
scanf("%d",&steps);
}while(steps<=0);
/* Are we moving the branch towards the (code) root?*/
to_false_root=(to==0)?0:1;
/* Work out where root node is relative to movingnode.
* Needed to work out whether to increase or decrease branch
* lengths when moving node*/
to_root=to_false_root; /* Correct unless we are between the
* two roots in the tree */
/* If we have a genetic root...*/
if(ISMODE(ROOTED)){
/* Decide depending on whether the root is floating or not,
* which node it refers to*/
node_c=(ISMODE(NODEASROOT))?branch[root]->node[0]:branch[root];
/* Iterate from the genetic root to the code root and set
* "to_root" as appropriate. to_root only differs from to_false_root
* if we are moving a branch between the two roots*/
while(node_c!=tree){
/* If we reach movingnode without passing either the to or from
* node first, then we must have come down on of the other branches
* or our root is the movingnode itself. In either case, we can't
* keep evolutionary times fixed - problem*/
if(node_c==movingnode){
printf("Moving branch containing root - can't keep evolutionary times fixed\n");
exit(0);
}
/* We encounter the "to" node first and so must be moving
* towards the genetic root*/
if(node_c==movingnode->node[to]){
to_root=0;
break;
}
/* We encounter the from root first and so must be moving
* away from the genetic node*/
if(node_c==movingnode->node[from]){
to_root=1;
break;
}
/* Iterate up one step*/
node_c=node_c->node[0];
}
/* If the root is on the branch we are moving, bad things
* happen (TM) Moving the branch can't be done if evolutionary
* times are fixed.
* We have deal with the case when root is on the moving bit of
* tree but not the false root.*/
if(slippe==0){
/* Decide where the root is depending on whether it is fixed
* or floating*/
node_c=(ISMODE(NODEASROOT))?branch[root]->node[0]:branch[root];
a=0;
/* We may assume that the code root is on the moving branch of
* the tree. If we have to pass through movingnode to get from
* the genetic root to the code root then we are fine*/
while(node_c!=tree){
if(node_c==movingnode){
a=1;
break;
}
node_c=node_c->node[0];
}
/* One special case if the movingnode is the fixed root*/
if(ISMODE(NODEASROOT) && branch[root]->node[0]==movingnode)
a=0;
/* If both the code and genetic roots are on the moving section
* of tree, complain*/
if(a==0){
printf("Moving branch containing root - can't keep evolutionary"
" times fixed\n");
exit(0);
}
}
/* If the root of the tree is on the same branch as we are moving across
* then we'll have trouble when we cross it - give warning*/
if(NOTMODE(NODEASROOT)) /* genetic root is floating*/
if(to_root==0) /* we are heading towards it*/
/* Depending on whether we are going away or towards the
* code root, see if the genetic root is on the branch we are
* moving along*/
if((to_false_root==0 && branch[root]==movingnode)
||(to_false_root==1 && branch[root]->node[0]==movingnode))
fprintf(file_p,"# *** Root in branch moving across. Beware, here be dragons ***\n");
}
/* Dump some information to file informing user what we are about
* to do*/
fprintf(file_p,"#Results from sliding branch from %s to"
" %s along branch from %s to %s\n"
,movingnode->name,(movingnode->node[slippe])->name
,(movingnode->node[from])->name,(movingnode->node[to])->name);
fprintf(file_p,"#Distance moved towards %s\t%s\n",(movingnode->node[to])->name,outstring);
if(ISMODE(MATRICES))
fprintf(matrix_file_p,"#Matrices from sliding branch from %s to"
" %s along branch from %s to %s\n"
,movingnode->name,(movingnode->node[slippe])->name
,(movingnode->node[from])->name,(movingnode->node[to])->name);
if(sample_file_p!=NULL){
fprintf(sample_file_p,"#Points %d\n",steps);
fprintf(sample_file_p,"#Samples from sliding branch from %s to"
" %s along branch from %s to %s\n"
,movingnode->name,(movingnode->node[slippe])->name
,(movingnode->node[from])->name,(movingnode->node[to])->name);
}
if(ISMODE(PROBS))
fprintf(prob_file_p,"#Probabilities from sliding branch from %s to"
" %s along branch from %s to %s\n"
,movingnode->name,(movingnode->node[slippe])->name
,(movingnode->node[from])->name,(movingnode->node[to])->name);
/* l is the total length of the "branch" we are moving across*/
l=movingnode->length[to]+movingnode->length[from];
if(steps==1)
f=f_min;
else
f=(f_max-f_min)/(steps-1);
/* We aren't changing any rates, so we don't need to apply the
* factor to any information (so factor=1)*/
factor=1.0;
factor_flag=0;
/* Initialise the tree...*/
movingnode->length[to]-=f_min;
if(to==0){
b=findnode(movingnode->node[0],movingnode);
(movingnode->node[to])->length[b]=movingnode->length[to];
}
else
(movingnode->node[to])->length[0]=movingnode->length[to];
movingnode->length[from]+=f_min;
if(from==0){
b=findnode(movingnode->node[0],movingnode);
(movingnode->node[from])->length[b]=movingnode->length[from];
}
else
(movingnode->node[from])->length[0]=movingnode->length[from];
/* If the tree is rooted, then we must preserve evolutionary
* times. This requires adding bits onto any other branches
* connected to the moving node, bar the to and from branches.*/
if(ISMODE(ROOTED)){
/* Case moving towards the evolutionary root - all branches
* connected to the moving node, bar from and to need to have
* the distance added onto them*/
sp_case=(movingnode==tree)?1:0;
if(to_root==0){
if(sp_case==1 && to!=0 && from!=0){
b=findnode(movingnode->node[0],movingnode);
movingnode->length[0]+=f_min;
(movingnode->node[0])->length[b]=movingnode->length[0];
}
for(a=sp_case;a<DOODAH && movingnode->node[a]!=NULL;a++)
if(a!=to && a!=from){
(movingnode->node[a])->length[0]+=f_min;
movingnode->length[a]=(movingnode->node[a])->length[0];
}
}
/* Else we are moving away from it and all branches connected to
* the moving node need the distance subtracted from them. Same
* special case as above*/
else{
if(sp_case==1 && to!=0 && from!=0){
b=findnode(movingnode->node[0],movingnode);
movingnode->length[0]-=f_min;
(movingnode->node[0])->length[b]=movingnode->length[0];
}
for(a=sp_case;a<DOODAH && movingnode->node[a]!=NULL;a++)
if(a!=to && a!=from){
(movingnode->node[a])->length[0]-=f_min;
movingnode->length[a]=(movingnode->node[a])->length[0];
}
}
}
for(c=0;c<steps;c++){
/* Adding new lengths - if any of the markers are zero then
* we have to search for the correct pointer in the parent node*/
movingnode->length[to]-=(c!=0)*f;
/* Also need to update length of branch that leads to this
* one. If to=0 then we must look up the tree*/
if(to==0){
b=findnode(movingnode->node[0],movingnode);
(movingnode->node[to])->length[b]=movingnode->length[to];
}
else
(movingnode->node[to])->length[0]=movingnode->length[to];
movingnode->length[from]+=(c!=0)*f;
/* Also need to update length of branch that leads to this
* one. If from=0 then we must look up the tree*/
if(from==0){
b=findnode(movingnode->node[0],movingnode);
(movingnode->node[from])->length[b]=movingnode->length[from];
}
else
(movingnode->node[from])->length[0]=movingnode->length[from];
/* If the tree is rooted, then we must preserve evolutionary
* times. This requires adding bits onto any other branches
* connected to the moving node, bar the to and from branches.*/
if(ISMODE(ROOTED)){
/* Case moving towards the evolutionary root - all branches
* connected to the moving node, bar from and to need to have
* the distance added onto them*/
sp_case=(movingnode==tree)?1:0; /* Is the movingnode the code root?*/
if(to_root==0){
if(sp_case==1 && to!=0 && from!=0){
b=findnode(movingnode->node[0],movingnode);
movingnode->length[0]+=(c!=0)*f;
(movingnode->node[0])->length[b]=movingnode->length[0];
}
for(a=sp_case;a<DOODAH && movingnode->node[a]!=NULL;a++)
if(a!=to && a!=from){
(movingnode->node[a])->length[0]+=(c!=0)*f;
movingnode->length[a]=(movingnode->node[a])->length[0];
}
}
/* Else we are moving away from it and all branches connected to
* the moving node need the distance subtracted from them. Same
* special case as above*/
else{
if(sp_case==1 && to!=0 && from!=0){
b=findnode(movingnode->node[0],movingnode);
movingnode->length[0]-=(c!=0)*f;
(movingnode->node[0])->length[b]=movingnode->length[0];
}
for(a=sp_case;a<DOODAH && movingnode->node[a]!=NULL;a++)
if(a!=to && a!=from){
(movingnode->node[a])->length[0]-=(c!=0)*f;
movingnode->length[a]=(movingnode->node[a])->length[0];
}
}
}
/* Fill in second copy of tree from first and update the leaf
* array to point to tree*/
filltree(tree,tree2,0);
leaves=0;
doleaf(tree,0);
/* Print a bit of information to all open files*/
printf("Doing distance %E\n",c*f+f_min);
if(ISMODE(TREES))
print_tree(tree,file_p,0);
fprintf(file_p,"%E\n",c*f+f_min);
if(ISMODE(MATRICES)){
fprintf(matrix_file_p,"\n#Distance %E\n",c*f+f_min);
if(ISMODE(TREES))
print_tree(tree,matrix_file_p,0);
}
if(ISMODE(VARIANCE)){
fprintf(variance_file_p,"\n#Distance %E\n",c*f+f_min);
if(ISMODE(TREES))
print_tree(tree,variance_file_p,0);
}
if(sample_file_p!=NULL){
fprintf(sample_file_p,"\n#Distance %E\n",c*f+f_min);
if(ISMODE(TREES))
print_tree(tree,sample_file_p,0);
}
if(ISMODE(PROBS)){
fprintf(prob_file_p,"\n#Distance %E\n",c*f+f_min);
if(ISMODE(TREES))
print_tree(tree,prob_file_p,0);
}
det=find_information(tree,tree2,e,factor_flag,factor);
/* Possible may want to print out more than one result*/
b=1;
if(ISMODE(INDIVIDUAL))
b=individual;
if(ISMODE(INDIVIDUAL)){
if(ISMODE(DETINDIV)){
fprintf(file_p,"\t\t\t%E\tD(",det[0]);
for(a=0;a<b-1;a++)
fprintf(file_p,"%d,",interesting_branches[a]);
fprintf(file_p,"%d)\n",interesting_branches[a]);
}else
for(a=0;a<b;a++)
fprintf(file_p,"\t\t\t%E\t%d\n",det[a],interesting_branches[a]);
}else
fprintf(file_p,"\t\t\t%E\tD\n",det[0]);
if(ISMODE(HKY) && NOTMODE(NOKAPPA) && NOTMODE(PERCENTILE))
fprintf(file_p,"\t\t\t%E\tKappa\n",det[b]);
free(det);
}
}
/* Routine to vary the length of one branch though several
* multipliers. This has little meaning when considering a clock-like
* (rooted) tree*/
void growbranch(struct treenode *node_p,FILE *file_p,unsigned int e){
#include "variables.h"
int steps,a,b,c;
int elastic;
double f_min,f_max,f;
struct treenode *tree;
/* Test to see whether tree is rooted - changing branch
* length in unrooted trees doesn't have much experimental
* meaning */
if(((mode&4)|(mode&32))!=0)
printf("\a\n**Changing branch length in a rooted tree doesn't"
" have meaning\n**in an experimental design problem!\n\n\a");
/* Make two copies of the tree*/
tree2=treecopy(node_p,0);
tree=treecopy(node_p,0);
/* Fill in the first*/
filltree(node_p,tree,0);
/* Choose branch to stretch - better be elastic*/
printf("\n");
for(a=0;a<branches;a++)
printf("Branch %d goes from %s to %s\n",a
,(branch[a]->node[0])->name,branch[a]->name);
do{
printf("\nWhich branch would you like to alter?");
scanf("%d",&elastic);
}while(elastic<0 || elastic>branches);
/* Get length scaling factors from user*/
printf("Altering length of a branch leading to"
" %s by a varying factor\n\n",branch[elastic]->name);
printf("Please enter min. factor, max factor and number of points:\n");
do{
printf("\tmin. factor:");
scanf("%lf",&f_min);
}while(f_min<=0);
do{
printf("\tmax. factor:");
scanf("%lf",&f_max);
}while(f_min>=f_max);
do{
printf("\tnumber of points:");
scanf("%d",&steps);
}while(steps<=0);
/* Dump the necessary information to file*/
fprintf(file_p,"#Results from varying length of branch"
" between %s and %s by factor\n"
,(branch[elastic]->node[0])->name,branch[elastic]->name);
fprintf(file_p,"#Factor\t\t\t%s\n",outstring);
if(ISMODE(MATRICES))
fprintf(matrix_file_p,"#Matrices from varying length of branch"
" between %s and %s by factor\n"
,(branch[elastic]->node[0])->name,branch[elastic]->name);
if(sample_file_p!=NULL){
fprintf(sample_file_p,"#Points %d\n",steps);
fprintf(sample_file_p,"#Samples from varying length of branch"
" between %s and %s by factor\n"
,(branch[elastic]->node[0])->name,branch[elastic]->name);
}
if(ISMODE(PROBS))
fprintf(prob_file_p,"#Probabilities from varying length of branch"
" between %s and %s by factor\n"
,(branch[elastic]->node[0])->name,branch[elastic]->name);
/* Main loop to stretch the branch*/
for(c=0;c<steps;c++){
/* Calculate the factor wanted and set the flag - we only
* want to apply the factor to one of the informations this
* time*/
if(steps==1)
f=f_min;
else
f=f_min+c*(f_max-f_min)/(steps-1);
factor=f;
factor_flag=elastic;
/* Fill in first copy from the original*/
filltree(node_p,tree,0);
/* Branch[] points to those of 'tree'
* Change length of the branch by factor - need to find the node
* that points from the other side of the branch.*/
branch[elastic]->length[0]=branch[elastic]->length[0]*f;
a=findnode(branch[elastic]->node[0],branch[elastic]);
(branch[elastic]->node[0])->length[a]=branch[elastic]->length[0];
/* Fill in the second copy from the first (with the new branch
* length and set all the leaves to point to "tree"*/
filltree(tree,tree2,0);
leaves=0;
doleaf(tree,0);
printf("Doing Factor %E\n",f);
/* If we are printing out the intermediate trees, then dump them
* to every file*/
if(ISMODE(TREES))
print_tree(tree,file_p,0);
fprintf(file_p,"%E\n",f);
if(ISMODE(MATRICES)){
fprintf(matrix_file_p,"\n#Factor %E\n",f);
if(ISMODE(TREES))
print_tree(tree,matrix_file_p,0);
}
if(ISMODE(VARIANCE)){
fprintf(variance_file_p,"\n#Factor %E\n",f);
if(ISMODE(TREES))
print_tree(tree,variance_file_p,0);
}
if(sample_file_p!=NULL){
fprintf(sample_file_p,"\n#Factor %E\n",f);
if(ISMODE(TREES))
print_tree(tree,sample_file_p,0);
}
if(ISMODE(PROBS)){
fprintf(prob_file_p,"\n#Factor %E\n",f);
if(ISMODE(TREES))
print_tree(tree,prob_file_p,0);
}
det=find_information(tree,tree2,e,factor_flag,factor);
/* Possible may want to print out more than one result*/
b=1;
if(ISMODE(INDIVIDUAL))
b=individual;
if(ISMODE(INDIVIDUAL)){
if(ISMODE(DETINDIV)){
fprintf(file_p,"\t\t\t%E\tD(",det[0]);
for(a=0;a<b-1;a++)
fprintf(file_p,"%d,",interesting_branches[a]);
fprintf(file_p,"%d)\n",interesting_branches[a]);
}else
for(a=0;a<b;a++)
fprintf(file_p,"\t\t\t%E\t%d\n",det[a],interesting_branches[a]);
}else
fprintf(file_p,"\t\t\t%E\tD\n",det[0]);
if(ISMODE(HKY) && NOTMODE(NOKAPPA) && NOTMODE(PERCENTILE))
fprintf(file_p,"\t\t\t%E\tKappa\n",det[b]);
free(det);
}
}
long anneal(Treestack *bstackp, const Branch *const inittree, long root,
const double t0, const double t1, const long maxaccept, const long maxpropose,
const long maxfail, FILE *const lenfp, unsigned char **bmat, long m, long n,
const long *weights, long *current_iter, Lvb_bool log_progress)
/* seek parsimonious tree from initial tree in inittree (of root root)
* with initial temperature t0, and subsequent temperatures obtained by
* multiplying the current temperature by (t1 / t0) ** n * t0 where n is
* the ordinal number of this temperature, after at least maxaccept changes
* have been accepted or maxpropose changes have been proposed, whichever is
* sooner;
* return the length of the best tree(s) found after maxfail consecutive
* temperatures have led to no new accepted solution;
* lenfp is for output of current tree length and associated details;
* *current_iter should give the iteration number at the start of this call and
* will be used in any statistics sent to lenfp, and will be updated on
* return */
{
long accepted = 0; /* changes accespted */
Lvb_bool dect; /* should decrease temperature */
double deltah; /* change in energy (1 - C.I.) */
long deltalen; /* change in length with new tree */
long failedcnt = 0; /* "failed count" for temperatures */
long iter = 0; /* iteration of mutate/evaluate loop */
long len; /* length of current tree */
long prev_len = UNSET; /* length of previous tree */
long lenbest; /* bet length found so far */
long lendash; /* length of proposed new tree */
long lenmin; /* minimum length for any tree */
double ln_t; /* ln(current temperature) */
long t_n = 0; /* ordinal number of current temperature */
Lvb_bool newtree; /* accepted a new configuration */
double pacc; /* prob. of accepting new config. */
Lvb_bool probaccd; /* have accepted based on Pacc */
long proposed = 0; /* trees proposed */
double r_lenmin; /* minimum length for any tree */
long rootdash; /* root of new configuration */
double t = t0; /* current temperature */
double t1_to_t0; /* T1:T0 ratio */
Branch *x; /* current configuration */
Branch *xdash; /* proposed new configuration */
extern Dataptr matrix; /* data matrix */
/* "local" dynamic heap memory */
x = treealloc(brcnt(matrix->n), matrix->m);
xdash = treealloc(brcnt(matrix->n), matrix->m);
treecopy(x, inittree); /* current configuration */
len = getplen(x, root, m, n, weights);
dect = LVB_FALSE; /* made LVB_TRUE as necessary at end of loop */
/* if t1_to_t0 is going to be very small, set it to zero without
* calculating it, to avoid underflow. Use this relation:
* if T1 / T0 < eps,
* ln (T1/T0) < ln eps
* i.e.,
* ln T1 - ln T0 < ln eps */
lvb_assert ((t0 >= LVB_EPS) && (t1 >= LVB_EPS) && (t1 <= t0)
&& (t0 <= 1.0));
if (log_wrapper(t1) - log_wrapper(t0) < log_wrapper(LVB_EPS))
t1_to_t0 = 0.0;
else
t1_to_t0 = t1 / t0;
lenbest = len;
treestack_push(bstackp, inittree, root); /* init. tree initially best */
if ((log_progress == LVB_TRUE) && (*current_iter == 0))
{
fprintf(lenfp, "\nRearrangement: Length:\n");
}
lenmin = getminlen(matrix);
r_lenmin = (double) lenmin;
while (1)
{
if ((log_progress == LVB_TRUE) && ((len != prev_len)
|| ((*current_iter % STAT_LOG_INTERVAL) == 0)))
{
lenlog(lenfp, *current_iter, len);
}
prev_len = len;
*current_iter += 1;
/* occasionally re-root, to prevent influence from root position */
if ((*current_iter % REROOT_INTERVAL) == 0)
root = arbreroot(x, root);
lvb_assert(t > DBL_EPSILON);
newtree = LVB_FALSE;
probaccd = LVB_FALSE;
/* mutation: alternate between the two mutation functions */
if (iter % 2)
{
rootdash = root;
mutate_spr(xdash, x, root); /* global change */
}
else
{
rootdash = root;
mutate_nni(xdash, x, root); /* local change */
}
lendash = getplen(xdash, rootdash, m, n, weights);
lvb_assert (lendash >= 1L);
deltalen = lendash - len;
deltah = (r_lenmin / (double) len) - (r_lenmin / (double) lendash);
if (deltah > 1.0) /* getminlen() problem with ambiguous sites */
deltah = 1.0;
if (deltalen <= 0) /* accept the change */
{
if (lendash <= lenbest) /* store tree if new */
{
if (lendash < lenbest) /* very best so far */
treestack_clear(bstackp); /* discard old bests */
if (treestack_push(bstackp, xdash, rootdash) == 1)
newtree = LVB_TRUE; /* new */
}
/* update current tree and its stats */
prev_len = len;
len = lendash;
treeswap(&x, &root, &xdash, &rootdash);
if (lendash < lenbest) /* very best so far */
lenbest = lendash;
}
else /* poss. accept change for the worse */
{
/* Mathematically,
* Pacc = e ** (-1/T * deltaH)
* therefore ln Pacc = -1/T * deltaH
*
* Computationally, if Pacc is going to be small, we
* can assume Pacc is 0 without actually working it
* out.
* i.e.,
* if ln Pacc < ln eps, let Pacc = 0
* substituting,
* if -deltaH / T < ln eps, let Pacc = 0
* rearranging,
* if -deltaH < T * ln eps, let Pacc = 0
* This lets us work out whether Pacc will be very
* close to zero without dividing anything by T. This
* should prevent overflow. Since T is no less
* than eps and ln eps is going to have greater
* magnitude than eps, underflow when calculating
* T * ln eps is not possible. */
if (-deltah < t * log_wrapper(LVB_EPS))
{
pacc = 0.0;
/* Call uni() even though its not required. It
* would have been called in LVB 1.0A, so this
* helps make results identical to results with
* that version. */
(void) uni();
}
else /* possibly accept the change */
{
pacc = exp_wrapper(-deltah/t);
if (uni() < pacc) /* do accept the change */
{
probaccd = LVB_TRUE;
treeswap(&x, &root, &xdash, &rootdash);
}
}
if (probaccd == LVB_TRUE)
{
prev_len = len;
len = lendash;
}
}
proposed++;
if (newtree == LVB_TRUE)
accepted++;
/* decide whether to reduce temperature */
if (accepted >= maxaccept) /* enough new trees */
{
failedcnt = 0; /* this temperature a 'success' */
dect = LVB_TRUE;
}
else if (proposed >= maxpropose) /* enough proposals */
{
failedcnt++;
if (failedcnt >= maxfail) /* system frozen */
break; /* end of cooling */
else /* decrease temp. */
dect = LVB_TRUE;
}
if (dect == LVB_TRUE)
{
t_n++; /* originally n is 0 */
/* near the start of the function we ensure t1_to_t0 is
* either zero or no less than LVB_EPS */
if (t1_to_t0 < LVB_EPS)
t = LVB_EPS;
else
{
ln_t = ((double) t_n) * log_wrapper(t1_to_t0) + log_wrapper(t0);
if (ln_t < log_wrapper(LVB_EPS))
t = LVB_EPS;
else
t = pow_wrapper(t1_to_t0, (double) t_n) * t0;
}
proposed = 0;
accepted = 0;
dect = LVB_FALSE;
}
iter++;
}
/* free "local" dynamic heap memory */
free(x);
free(xdash);
return lenbest;
} /* end anneal() */
