/*swapping across edge whose head is v*/
void bNNIupdateAverages(double **A, node *v, edge *par, edge *skew,
edge *swap, edge *fixed)
{
A[v->index][v->index] = 0.25*(A[fixed->head->index][par->head->index] +
A[fixed->head->index][swap->head->index] +
A[skew->head->index][par->head->index] +
A[skew->head->index][swap->head->index]);
updateSubTreeAfterNNI(A, v, fixed, skew->head, swap->head, 0.25, UP);
updateSubTreeAfterNNI(A, v, par, swap->head, skew->head, 0.25, DOWN);
updateSubTreeAfterNNI(A, v, skew, fixed->head, par->head, 0.25, UP);
updateSubTreeAfterNNI(A, v, swap, par->head, fixed->head, 0.25, SKEW);
}
/*Idea is: we are looking at the subtree rooted at rootEdge. The subtree
rooted at closer is closer to rootEdge after the NNI, while the subtree
rooted at further is further to rootEdge after the NNI. direction tells
the direction of the NNI with respect to rootEdge*/
void updateSubTreeAfterNNI(double **A, meNode *v, meEdge *rootEdge, meNode *closer, meNode *further,
double dcoeff, int direction)
{
meEdge *sib;
switch(direction)
{
case UP: /*rootEdge is below the center edge of the NNI*/
/*recursive calls to subtrees, if necessary*/
if (NULL != rootEdge->head->leftEdge)
updateSubTreeAfterNNI(A, v, rootEdge->head->leftEdge, closer, further, 0.5*dcoeff,UP);
if (NULL != rootEdge->head->rightEdge)
updateSubTreeAfterNNI(A, v, rootEdge->head->rightEdge, closer, further, 0.5*dcoeff,UP);
updatePair(A, rootEdge, rootEdge, closer, further, dcoeff, UP);
sib = siblingEdge(v->parentEdge);
A[rootEdge->head->index][v->index] =
A[v->index][rootEdge->head->index] =
0.5*A[rootEdge->head->index][sib->head->index] +
0.5*A[rootEdge->head->index][v->parentEdge->tail->index];
break;
case DOWN: /*rootEdge is above the center edge of the NNI*/
sib = siblingEdge(rootEdge);
if (NULL != sib)
updateSubTreeAfterNNI(A, v, sib, closer, further, 0.5*dcoeff, SKEW);
if (NULL != rootEdge->tail->parentEdge)
updateSubTreeAfterNNI(A, v, rootEdge->tail->parentEdge, closer, further, 0.5*dcoeff, DOWN);
updatePair(A, rootEdge, rootEdge, closer, further, dcoeff, DOWN);
A[rootEdge->head->index][v->index] =
A[v->index][rootEdge->head->index] =
0.5*A[rootEdge->head->index][v->leftEdge->head->index] +
0.5*A[rootEdge->head->index][v->rightEdge->head->index];
break;
case SKEW: /*rootEdge is in subtree skew to v*/
if (NULL != rootEdge->head->leftEdge)
updateSubTreeAfterNNI(A, v, rootEdge->head->leftEdge, closer, further, 0.5*dcoeff,SKEW);
if (NULL != rootEdge->head->rightEdge)
updateSubTreeAfterNNI(A, v, rootEdge->head->rightEdge, closer, further, 0.5*dcoeff,SKEW);
updatePair(A, rootEdge, rootEdge, closer, further, dcoeff, UP);
A[rootEdge->head->index][v->index] =
A[v->index][rootEdge->head->index] =
0.5*A[rootEdge->head->index][v->leftEdge->head->index] +
0.5*A[rootEdge->head->index][v->rightEdge->head->index];
break;
}
}
