boolean treeEvaluate (tree *tr, double smoothFactor) /* Evaluate a user tree */
{
boolean result;
if(tr->useBrLenScaler)
assert(0);
result = smoothTree(tr, (int)((double)smoothings * smoothFactor));
assert(result);
evaluateGeneric(tr, tr->start);
return TRUE;
}
int main(int argc, char * argv[])
{
tree * tr;
if (argc != 2)
{
fprintf (stderr, "syntax: %s [binary-alignment-file]\n", argv[0]);
return (1);
}
tr = (tree *)malloc(sizeof(tree));
/* read the binary input, setup tree, initialize model with alignment */
read_msa(tr,argv[1]);
tr->randomNumberSeed = 665;
makeRandomTree(tr);
printf("Number of taxa: %d\n", tr->mxtips);
printf("Number of partitions: %d\n", tr->NumberOfModels);
/* compute the LH of the full tree */
printf ("Virtual root: %d\n", tr->start->number);
evaluateGeneric(tr, tr->start, TRUE);
printf("Likelihood: %f\n", tr->likelihood);
/* 8 rounds of branch length optimization */
smoothTree(tr, 1);
evaluateGeneric(tr, tr->start, TRUE);
printf("Likelihood after branch length optimization: %.20f\n", tr->likelihood);
/* Now we show how to find a particular LH vector for a node */
int i;
int node_number = tr->mxtips + 1;
nodeptr p = tr->nodep[node_number];
printf("Pointing to node %d\n", p->number);
/* Fix as VR */
newviewGeneric(tr, p, FALSE);
newviewGeneric(tr, p->back, FALSE);
evaluateGeneric(tr, p, FALSE);
printf("Likelihood : %.f\n", tr->likelihood);
printf("Make a copy of LH vector for node %d\n", p->number);
likelihood_vector *vector = copy_likelihood_vectors(tr, p);
for(i=0; i<vector->num_partitions; i++)
printf("Partition %d requires %d bytes\n", i, (int)vector->partition_sizes[i]);
/* Check we have the same vector in both tree and copied one */
assert(same_vector(tr, p, vector));
/* Now force the p to get a new value (generally branch lengths are NOT updated like this) */
/* This is just an example to show usage (for fast NNI eval), manually updating vectors is not recommended! */
printf("bl : %.40f\n", p->next->z[0]);
p->next->z[0] = p->next->back->z[0] = zmin;
printf("bl : %.40f\n", p->next->z[0]);
newviewGeneric(tr, p, FALSE);
assert(!same_vector(tr, p, vector));
evaluateGeneric(tr, p, FALSE);
printf("Likelihood : %f\n", tr->likelihood);
restore_vector(tr, p, vector);
assert(same_vector(tr, p, vector));
evaluateGeneric(tr, p, FALSE);
printf("Likelihood after manually restoring the vector : %f\n", tr->likelihood);
free_likelihood_vector(vector);
/* Pick an inner branch */
printf("numBranches %d \n", tr->numBranches);
//tr->numBranches = 1;
p = tr->nodep[tr->mxtips + 1];
int partition_id = 0; /* single partition */
double bl = get_branch_length(tr, p, partition_id);
printf("z value: %f , bl value %f\n", p->z[partition_id], bl);
/* set the bl to 2.5 */
double new_bl = 2.5;
set_branch_length(tr, p, partition_id, new_bl);
printf("Changed BL to %f\n", new_bl);
printf("new z value: %f , new bl value %f\n", p->z[partition_id], get_branch_length(tr, p, partition_id));
/* set back to original */
printf("Changed to previous BL\n");
set_branch_length(tr, p, partition_id, bl);
printf("new z value: %f , new bl value %f\n", p->z[partition_id], get_branch_length(tr, p, partition_id));
return (0);
}