void assignUpWeights(edge *etest, node *vtest, node *va, edge *back, node *cprev, double oldD_AB, double coeff, double **A,
double ***swapWeights)
{
/*SPR performed on tree above vtest...*/
/*same idea as above, with appropriate selections of edges and nodes*/
edge *sib, *left, *right;
/*B is above vtest, A is other tree below vtest unioned with trees in path to vtest*/
/*sib is tree C being passed by B*/
/*D is tree below etest*/
double D_AB, D_CD, D_AC, D_BD;
// double thisWeight; deleted by EP, 2013-09-16, also below
sib = siblingEdge(etest);
left = etest->head->leftEdge;
right = etest->head->rightEdge;
if (NULL == back) /*first recursive call*/
{
if (NULL == left)
return;
else /*start the process of assigning weights recursively*/
{
assignUpWeights(left,vtest,va,etest,va,A[va->index][vtest->index],0.5,A,swapWeights);
assignUpWeights(right,vtest,va,etest,va,A[va->index][vtest->index],0.5,A,swapWeights);
}
}
else /*second or later recursive call*/
{
D_BD = A[vtest->index][etest->head->index];
D_CD = A[sib->head->index][etest->head->index];
D_AC = A[back->head->index][sib->head->index] + coeff*(A[va->index][sib->head->index] - A[vtest->index][sib->head->index]);
D_AB = 0.5*(oldD_AB + A[vtest->index][cprev->index]);
// thisWeight = deleted by EP, 2013-09-16
swapWeights[1][vtest->index][etest->head->index] = swapWeights[1][vtest->index][back->head->index] + (D_AC + D_BD - D_AB - D_CD);
if (NULL != left)
{
assignUpWeights(left,vtest, va, etest, sib->head, D_AB, 0.5*coeff, A, swapWeights);
assignUpWeights(right,vtest, va, etest, sib->head, D_AB, 0.5*coeff, A, swapWeights);
}
}
}
void BalWFext(meEdge *e, double **A) /*works except when e is the one edge
inserted to new vertex v by firstInsert*/
{
meEdge *f, *g;
if ((leaf(e->head)) && (leaf(e->tail)))
e->distance = A[e->head->index][e->head->index];
else if (leaf(e->head))
{
f = e->tail->parentEdge;
g = siblingEdge(e);
e->distance = 0.5*(A[e->head->index][g->head->index]
+ A[e->head->index][f->head->index]
- A[g->head->index][f->head->index]);
}
else
{
f = e->head->leftEdge;
g = e->head->rightEdge;
e->distance = 0.5*(A[g->head->index][e->head->index]
+ A[f->head->index][e->head->index]
- A[f->head->index][g->head->index]);
}
}
void assignDownWeightsDown (edge *etest, node *vtest, node *va, edge *back,
node *cprev, double oldD_AB, double coeff, double **A, double ***swapWeights)
{
/* again the same general idea */
edge *sib, *left, *right;
/* sib here = par in assignDownWeightsSkew
* rest is the same as assignDownWeightsSkew */
double D_AB, D_CD, D_AC, D_BD;
/* B is below vtest, A is below va unioned with all trees already passed by B
* C is subtree being passed - below sib
* D is tree below etest */
sib = siblingEdge (etest);
left = etest->head->leftEdge;
right = etest->head->rightEdge;
D_BD = A[vtest->index][etest->head->index];
D_CD = A[sib->head->index][etest->head->index];
D_AC = A[sib->head->index][back->head->index] +
coeff * (A[sib->head->index][va->index] -
A[sib->head->index][vtest->index]);
D_AB = 0.5 * (oldD_AB + A[vtest->index][cprev->index]);
swapWeights[0][vtest->index][etest->head->index] =
swapWeights[0][vtest->index][back->head->index] +
( D_AC + D_BD - D_AB - D_CD);
if (NULL != left)
{
assignDownWeightsDown (left, vtest, va, etest, sib->head, D_AB,
0.5 * coeff, A, swapWeights);
assignDownWeightsDown (right, vtest, va, etest, sib->head, D_AB,
0.5 * coeff, A, swapWeights);
}
return;
}
void bNNItopSwitch(meTree *T, meEdge *e, int direction, double **A)
{
meEdge *down, *swap, *fixed;
meNode *u, *v;
if (verbose)
{
printf("Performing branch swap across edge %s ",e->label);
printf("with ");
if (LEFT == direction)
printf("left ");
else printf("right ");
printf("subtree.\n");
}
down = siblingEdge(e);
u = e->tail;
v = e->head;
if (LEFT == direction)
{
swap = e->head->leftEdge;
fixed = e->head->rightEdge;
v->leftEdge = down;
}
else
{
swap = e->head->rightEdge;
fixed = e->head->leftEdge;
v->rightEdge = down;
}
swap->tail = u;
down->tail = v;
if(e->tail->leftEdge == e)
u->rightEdge = swap;
else
u->leftEdge = swap;
bNNIupdateAverages(A, v, e->tail->parentEdge, down, swap, fixed);
}
void TBR(tree *T, double **D, double **A)
{
int i;
edge *esplit, *etop, *eBestTop, *eBestBottom, *eBestSplit;
edge *eout, *block;
edge *left, *right, *par, *sib;
double **dXTop; /*dXTop[i][j] is average distance from subtree rooted at i to tree above split edge, if
SPR above split edge cuts edge whose head has index j*/
double bestWeight;
double ***TBRWeights;
dXTop = initDoubleMatrix(T->size);
weighTree(T);
TBRWeights = (double ***)calloc(T->size,sizeof(double **));
for(i=0;i<T->size;i++)
TBRWeights[i] = initDoubleMatrix(T->size);
do
{
zero3DMatrix(TBRWeights,T->size,T->size,T->size);
bestWeight = 0.0;
eBestSplit = eBestTop = eBestBottom = NULL;
for(esplit=depthFirstTraverse(T,NULL);NULL!=esplit;esplit=depthFirstTraverse(T,esplit))
{
par = esplit->tail->parentEdge;
if (NULL != par)
{
sib = siblingEdge(esplit);
/*next two lines calculate the possible improvements for any SPR above esplit*/
assignTBRDownWeightsUp(par,esplit->head,sib->head,NULL,NULL,0.0,1.0,A,TBRWeights,&bestWeight,&eBestSplit,&eBestTop,&eBestBottom);
assignTBRDownWeightsSkew(sib,esplit->head,sib->tail,NULL,NULL,0.0,1.0,A,TBRWeights,&bestWeight,&eBestSplit,&eBestTop,&eBestBottom);
calcTBRaverages(T,esplit,A,dXTop); /*calculates the average distance from any subtree
below esplit to the entire subtree above esplit,
after any possible SPR above*/
/*for etop above esplit, we loop using information from above to calculate values
for all possible SPRs below esplit*/
}
right = esplit->head->rightEdge;
if (NULL != right)
{
left = esplit->head->leftEdge;
/*test case: etop = null means only do bottom SPR*/
assignTBRUpWeights(left,esplit->head,right->head,NULL,NULL,0.0,1.0,A,dXTop,TBRWeights,NULL,&bestWeight,&eBestSplit,&eBestTop,&eBestBottom);
assignTBRUpWeights(right,esplit->head,left->head,NULL,NULL,0.0,1.0,A,dXTop,TBRWeights,NULL,&bestWeight,&eBestSplit,&eBestTop,&eBestBottom);
block = esplit;
while (NULL != block)
{
if (block != esplit)
{
etop = block;
assignTBRUpWeights(left,esplit->head,right->head,NULL,NULL,0.0,1.0,A,dXTop,TBRWeights,etop,&bestWeight,&eBestSplit,&eBestTop,&eBestBottom);
assignTBRUpWeights(right,esplit->head,left->head,NULL,NULL,0.0,1.0,A,dXTop,TBRWeights,etop,&bestWeight,&eBestSplit,&eBestTop,&eBestBottom);
}
eout = siblingEdge(block);
if (NULL != eout)
{
etop = findBottomLeft(eout);
while (etop->tail != eout->tail)
{
/*for ebottom below esplit*/
assignTBRUpWeights(left,esplit->head,right->head,NULL,NULL,0.0,1.0,A,dXTop,TBRWeights,etop,&bestWeight,&eBestSplit,&eBestTop,&eBestBottom);
assignTBRUpWeights(right,esplit->head,left->head,NULL,NULL,0.0,1.0,A,dXTop,TBRWeights,etop,&bestWeight,&eBestSplit,&eBestTop,&eBestBottom);
etop = depthFirstTraverse(T,etop);
}
/*etop == eout*/
assignTBRUpWeights(left,esplit->head,right->head,NULL,NULL,0.0,1.0,A,dXTop,TBRWeights,etop,&bestWeight,&eBestSplit,&eBestTop,&eBestBottom);
assignTBRUpWeights(right,esplit->head,left->head,NULL,NULL,0.0,1.0,A,dXTop,TBRWeights,etop,&bestWeight,&eBestSplit,&eBestTop,&eBestBottom);
}
block = block->tail->parentEdge;
}
} /*if NULL != right*/
} /*for esplit*/
/*find bestWeight, best split edge, etc.*/
if (bestWeight < -EPSILON)
{
// if (verbose)
// {
// printf("TBR #%d: Splitting edge %s: top edge %s, bottom edge %s\n",*count+1,
// eBestSplit->label, eBestTop->label,eBestBottom->label);
// printf("Old tree weight is %lf, new tree weight should be %lf\n",T->weight, T->weight + 0.25*bestWeight);
// }
TBRswitch(T,eBestSplit,eBestTop,eBestBottom);
makeBMEAveragesTable(T,D,A);
assignBMEWeights(T,A);
weighTree(T);
// if (verbose)
// printf("TBR: new tree weight is %lf\n\n",T->weight);<
// (*count)++;
}
else
bestWeight = 1.0;
} while (bestWeight < -EPSILON);
for(i=0;i<T->size;i++)
freeMatrix(TBRWeights[i],T->size);
freeMatrix(dXTop,T->size);
}
void assignTBRUpWeights(edge *ebottom, node *vtest, node *va, edge *back, node *cprev, double oldD_AB, double coeff, double **A,
double **dXTop, double ***swapWeights, edge *etop, double *bestWeight,
edge **bestSplit, edge **bestTop, edge **bestBottom)
/*function assigns the value for etop if the tree below vtest is moved to be below etop*/
/*and SPR for tree bottom tree splits ebottom*/
/*recursive function searching over values of ebottom*/
/*minor variant of SPR.c's assignUpWeights
difference is the index assignment in the array swapWeights, which has a different meaning
for the TBR routines*/
/*also using dXTop to assign value of average distance to tree above vtest*/
{ /*SPR performed on tree above vtest...*/
edge *sib, *left, *right;
/*B is above vtest, A is other tree below vtest unioned with trees in path to vtest*/
/*sib is tree C being passed by B*/
/*D is tree below etest*/
double D_AB, D_CD, D_AC, D_BD;
sib = siblingEdge(ebottom);
left = ebottom->head->leftEdge;
right = ebottom->head->rightEdge;
if (NULL == etop)
{
if (NULL == back) /*first recursive call*/
{
if (NULL == left)
return; /*no subtree below for SPR*/
else /*NULL == back and NULL == etop*/
{
assignTBRUpWeights(left,vtest,va,ebottom,va,A[va->index][vtest->index],0.5,A,dXTop,swapWeights,NULL,bestWeight,bestSplit,bestTop,bestBottom);
assignTBRUpWeights(right,vtest,va,ebottom,va,A[va->index][vtest->index],0.5,A,dXTop,swapWeights,NULL,bestWeight,bestSplit,bestTop,bestBottom);
}
}
else /*NULL != back*/
{
D_BD = A[ebottom->head->index][vtest->index];
/*B is tree above vtest, D is tree below ebottom*/
D_CD = A[sib->head->index][ebottom->head->index]; /*C is tree below sib*/
D_AC = A[back->head->index][sib->head->index] +
coeff*(A[va->index][sib->head->index] - A[vtest->index][sib->head->index]);
/*va is root of subtree skew back at vtest*/
/*A is union of tree below va and all subtrees already passed in path from vtest to ebottom*/
D_AB = 0.5*(oldD_AB + A[vtest->index][cprev->index]);
swapWeights[vtest->index][ebottom->head->index][ebottom->head->index] = swapWeights[vtest->index][back->head->index][back->head->index] + (D_AC + D_BD - D_AB - D_CD);
if (swapWeights[vtest->index][ebottom->head->index][ebottom->head->index] < *bestWeight)
{
*bestSplit = vtest->parentEdge;
*bestTop = NULL;
*bestBottom = ebottom;
*bestWeight = swapWeights[vtest->index][ebottom->head->index][ebottom->head->index];
}
if (NULL != left)
{
assignTBRUpWeights(left,vtest,va,ebottom,sib->head,D_AB,0.5*coeff,A,dXTop,swapWeights,NULL,bestWeight,bestSplit,bestTop,bestBottom);
assignTBRUpWeights(right,vtest,va,ebottom,sib->head,D_AB,0.5*coeff,A,dXTop,swapWeights,NULL,bestWeight,bestSplit,bestTop,bestBottom);
}
}
}
else /*NULL != etop*/
{
if (NULL == back) /*first recursive call*/
{
if (swapWeights[vtest->index][etop->head->index][etop->head->index]< *bestWeight)
/*this represents value of SPR from esplit to etop, with no SPR in bottom tree*/
{
*bestSplit = vtest->parentEdge;
*bestTop = etop;
*bestBottom = NULL;
*bestWeight = swapWeights[vtest->index][etop->head->index][etop->head->index];
}
if (NULL == left)
return; /*no subtree below for SPR*/
else if (NULL != etop)/*start the process of assigning weights recursively*/
{
assignTBRUpWeights(left,vtest,va,ebottom,va,dXTop[va->index][etop->head->index],0.5,A,dXTop,swapWeights,etop,bestWeight,bestSplit,bestTop,bestBottom);
assignTBRUpWeights(right,vtest,va,ebottom,va,dXTop[va->index][etop->head->index],0.5,A,dXTop,swapWeights,etop,bestWeight,bestSplit,bestTop,bestBottom);
}
} /*NULL == back*/
/*in following bit, any average distance of form A[vtest->index][x->index] is
replaced by dXTop[x->index][etop->head->index]*/
else /*second or later recursive call, NULL != etop*/
{
D_BD = dXTop[ebottom->head->index][etop->head->index]; /*B is tree above vtest - it is in configuration
indexed by etop*/
/*D is tree below ebottom*/
D_CD = A[sib->head->index][ebottom->head->index]; /*C is tree below sib*/
D_AC = A[back->head->index][sib->head->index] +
coeff*(A[va->index][sib->head->index] - A[sib->head->index][vtest->index]);
/*it is correct to use A[][] here because the bad average distances involving B from the first term will
be cancelled by the bad average distances involving B in the subtracted part*/
/*va is root of subtree skew back at vtest*/
/*A is union of tree below va and all subtrees already passed in path from vtest to ebottom*/
D_AB = 0.5*(oldD_AB + dXTop[cprev->index][etop->head->index]);
swapWeights[vtest->index][ebottom->head->index][etop->head->index] = swapWeights[vtest->index][back->head->index][etop->head->index] + (D_AC + D_BD - D_AB - D_CD);
if (swapWeights[vtest->index][ebottom->head->index][etop->head->index] + swapWeights[vtest->index][etop->head->index][etop->head->index]< *bestWeight)
/*first term is contribution of second SPR, second term is contribution of first SPR*/
{
*bestSplit = vtest->parentEdge;
*bestTop = etop;
*bestBottom = ebottom;
*bestWeight = swapWeights[vtest->index][ebottom->head->index][etop->head->index] + swapWeights[vtest->index][etop->head->index][etop->head->index];
}
if (NULL != left)
{
assignTBRUpWeights(left,vtest, va, ebottom, sib->head, D_AB, 0.5*coeff, A, dXTop, swapWeights,etop,bestWeight,bestSplit,bestTop,bestBottom);
assignTBRUpWeights(right,vtest, va, ebottom, sib->head, D_AB, 0.5*coeff, A, dXTop, swapWeights,etop,bestWeight,bestSplit,bestTop,bestBottom);
}
} /*else NULL != back, etop*/
}
}
/* An inelegant iterative version */
void SPRUpShift (node *vmove, edge *esplit)
{
edge *f;
edge **EPath;
edge **sib;
node **v;
int i;
int pathLength;
for (f=esplit->tail->parentEdge,pathLength=1; f->tail != vmove; f=f->tail->parentEdge)
pathLength++;
/* count number of edges to vmove
* note that pathLength > 0 will hold */
EPath = (edge **) mCalloc (pathLength, sizeof(edge *));
v = (node **) mCalloc (pathLength, sizeof(edge *));
sib = (edge **) mCalloc ((pathLength+1), sizeof(edge *));
/* there are pathLength + 1 side trees, one at the head and tail of each edge in the path */
sib[pathLength] = siblingEdge (esplit);
i = pathLength;
f = esplit->tail->parentEdge;
while (i > 0)
{
i--;
EPath[i] = f;
sib[i] = siblingEdge (f);
v[i] = f->head;
f = f->tail->parentEdge;
}
/* indexed so head of Epath is v[i], tail is v[i-1] and sibling edge is sib[i]
* need to assign head, tail of each edge in path
* as well as have proper values for the left and right fields */
if (esplit == esplit->tail->leftEdge)
{
vmove->leftEdge = esplit;
vmove->rightEdge = EPath[pathLength-1];
}
else
{
vmove->rightEdge = esplit;
vmove->leftEdge = EPath[pathLength-1];
}
esplit->tail = vmove;
/* espilt->head remains unchanged
* vmove has the proper fields for left, right, and parentEdge */
for(i=0; i<(pathLength-1); i++)
EPath[i]->tail = v[i+1];
/* this bit flips the orientation along the path
* the tail of Epath[i] is now v[i+1] instead of v[i-1] */
EPath[pathLength-1]->tail = vmove;
for (i=1; i<pathLength; i++)
{
if (sib[i+1] == v[i]->leftEdge)
v[i]->rightEdge = EPath[i-1];
else
v[i]->leftEdge = EPath[i-1];
}
if (sib[1] == v[0]->leftEdge)
v[0]->rightEdge = sib[0];
else
v[0]->leftEdge = sib[0];
sib[0]->tail = v[0];
free(EPath);
free(v);
free(sib);
return;
}
int NNIEdgeTest(edge *e, tree *T, double **A, double *weight)
{
int a,b,c,d;
edge *f;
double *lambda;
double D_LR, D_LU, D_LD, D_RD, D_RU, D_DU;
double w1,w2,w0;
if ((leaf(e->tail)) || (leaf(e->head)))
return(NONE);
lambda = (double *)malloc(3*sizeof(double));
a = e->tail->parentEdge->topsize;
f = siblingEdge(e);
b = f->bottomsize;
c = e->head->leftEdge->bottomsize;
d = e->head->rightEdge->bottomsize;
lambda[0] = ((double) b*c + a*d)/((a + b)*(c+d));
lambda[1] = ((double) b*c + a*d)/((a + c)*(b+d));
lambda[2] = ((double) c*d + a*b)/((a + d)*(b+c));
D_LR = A[e->head->leftEdge->head->index][e->head->rightEdge->head->index];
D_LU = A[e->head->leftEdge->head->index][e->tail->index];
D_LD = A[e->head->leftEdge->head->index][f->head->index];
D_RU = A[e->head->rightEdge->head->index][e->tail->index];
D_RD = A[e->head->rightEdge->head->index][f->head->index];
D_DU = A[e->tail->index][f->head->index];
w0 = wf2(lambda[0],D_RU,D_LD,D_LU,D_RD,D_DU,D_LR);
w1 = wf2(lambda[1],D_RU,D_LD,D_DU,D_LR,D_LU,D_RD);
w2 = wf2(lambda[2],D_DU,D_LR,D_LU,D_RD,D_RU,D_LD);
free(lambda);
if (w0 <= w1)
{
if (w0 <= w2) /*w0 <= w1,w2*/
{
*weight = 0.0;
return(NONE);
}
else /*w2 < w0 <= w1 */
{
*weight = w2 - w0;
/* if (verbose)
{
printf("Swap across %s. ",e->label);
printf("Weight dropping by %lf.\n",w0 - w2);
printf("New weight should be %lf.\n",T->weight + w2 - w0);
}*/
return(RIGHT);
}
}
else if (w2 <= w1) /*w2 <= w1 < w0*/
{
*weight = w2 - w0;
/* if (verbose)
{
printf("Swap across %s. ",e->label);
printf("Weight dropping by %lf.\n",w0 - w2);
printf("New weight should be %lf.\n",T->weight + w2 - w0);
}*/
return(RIGHT);
}
else /*w1 < w2, w0*/
{
*weight = w1 - w0;
/* if (verbose)
{
printf("Swap across %s. ",e->label);
printf("Weight dropping by %lf.\n",w0 - w1);
printf("New weight should be %lf.\n",T->weight + w1 - w0);
}*/
return(LEFT);
}
}
//void NNI(tree *T, double **avgDistArray, int *count)
void NNI(tree *T, double **avgDistArray, int *count, double **D, int numSpecies)
{
edge *e, *centerEdge;
edge **edgeArray;
int *location;
int *p,*q;
int i,j;
int possibleSwaps;
double *weights;
p = initPerm(T->size+1);
q = initPerm(T->size+1);
edgeArray = (edge **) malloc((T->size+1)*sizeof(double));
weights = (double *) malloc((T->size+1)*sizeof(double));
location = (int *) malloc((T->size+1)*sizeof(int));
double epsilon = 0.0;
for (i=0; i<numSpecies; i++)
for (j=0; j<numSpecies; j++)
epsilon += D[i][j];
epsilon = (epsilon / (numSpecies * numSpecies)) * EPSILON;
for (i=0;i<T->size+1;i++)
{
weights[i] = 0.0;
location[i] = NONE;
}
e = findBottomLeft(T->root->leftEdge);
/* *count = 0; */
while (NULL != e)
{
edgeArray[e->head->index+1] = e;
location[e->head->index+1] =
NNIEdgeTest(e,T,avgDistArray,weights + e->head->index + 1);
e = depthFirstTraverse(T,e);
}
possibleSwaps = makeThreshHeap(p,q,weights,T->size+1,0.0);
permInverse(p,q,T->size+1);
/*we put the negative values of weights into a heap, indexed by p
with the minimum value pointed to by p[1]*/
/*p[i] is index (in edgeArray) of edge with i-th position
in the heap, q[j] is the position of edge j in the heap */
while (weights[p[1]] + epsilon < 0)
{
centerEdge = edgeArray[p[1]];
(*count)++;
T->weight = T->weight + weights[p[1]];
NNItopSwitch(T,edgeArray[p[1]],location[p[1]],avgDistArray);
location[p[1]] = NONE;
weights[p[1]] = 0.0; /*after the NNI, this edge is in optimal
configuration*/
popHeap(p,q,weights,possibleSwaps--,1);
/*but we must retest the other four edges*/
e = centerEdge->head->leftEdge;
NNIRetestEdge(p,q,e,T,avgDistArray,weights,location,&possibleSwaps);
e = centerEdge->head->rightEdge;
NNIRetestEdge(p,q,e,T,avgDistArray,weights,location,&possibleSwaps);
e = siblingEdge(centerEdge);
NNIRetestEdge(p,q,e,T,avgDistArray,weights,location,&possibleSwaps);
e = centerEdge->tail->parentEdge;
NNIRetestEdge(p,q,e,T,avgDistArray,weights,location,&possibleSwaps);
}
free(p);
free(q);
free(location);
free(edgeArray);
}
int bNNIEdgeTest(meEdge *e, meTree *T, double **A, double *weight)
{
meEdge *f;
double D_LR, D_LU, D_LD, D_RD, D_RU, D_DU;
double w1,w2,w0;
/*if (verbose)
printf("Branch swap: testing edge %s.\n",e->label);*/
if ((leaf(e->tail)) || (leaf(e->head)))
return(NONE);
f = siblingEdge(e);
D_LR = A[e->head->leftEdge->head->index][e->head->rightEdge->head->index];
D_LU = A[e->head->leftEdge->head->index][e->tail->index];
D_LD = A[e->head->leftEdge->head->index][f->head->index];
D_RU = A[e->head->rightEdge->head->index][e->tail->index];
D_RD = A[e->head->rightEdge->head->index][f->head->index];
D_DU = A[e->tail->index][f->head->index];
w0 = wf5(D_RU,D_LD,D_LU,D_RD,D_DU,D_LR); /*weight of current config*/
w1 = wf5(D_RU,D_LD,D_DU,D_LR,D_LU,D_RD); /*weight with L<->D switch*/
w2 = wf5(D_DU,D_LR,D_LU,D_RD,D_RU,D_LD); /*weight with R<->D switch*/
if (w0 <= w1)
{
if (w0 <= w2) /*w0 <= w1,w2*/
{
*weight = 0.0;
return(NONE);
}
else /*w2 < w0 <= w1 */
{
*weight = w2 - w0;
if (verbose)
{
printf("Possible swap across %s. ",e->label);
printf("Weight dropping by %lf.\n",w0 - w2);
printf("New weight would be %lf.\n",T->weight + w2 - w0);
}
return(RIGHT);
}
}
else if (w2 <= w1) /*w2 <= w1 < w0*/
{
*weight = w2 - w0;
if (verbose)
{
printf("Possible swap across %s. ",e->label);
printf("Weight dropping by %lf.\n",w0 - w2);
printf("New weight should be %lf.\n",T->weight + w2 - w0);
}
return(RIGHT);
}
else /*w1 < w2, w0*/
{
*weight = w1 - w0;
if (verbose)
{
printf("Possible swap across %s. ",e->label);
printf("Weight dropping by %lf.\n",w0 - w1);
printf("New weight should be %lf.\n",T->weight + w1 - w0);
}
return(LEFT);
}
}
int bNNIEdgeTest (edge *e, tree *T, double **A, double *weight)
{
edge *f;
double D_LR, D_LU, D_LD, D_RD, D_RU, D_DU;
double w1, w2, w0;
if ((leaf(e->tail)) || (leaf(e->head)))
return (NONE);
f = siblingEdge (e);
D_LR = A[e->head->leftEdge->head->index][e->head->rightEdge->head->index];
D_LU = A[e->head->leftEdge->head->index][e->tail->index];
D_LD = A[e->head->leftEdge->head->index][f->head->index];
D_RU = A[e->head->rightEdge->head->index][e->tail->index];
D_RD = A[e->head->rightEdge->head->index][f->head->index];
D_DU = A[e->tail->index][f->head->index];
w0 = wf5 (D_RU, D_LD, D_LU, D_RD, D_DU, D_LR); // weight of current config
w1 = wf5 (D_RU, D_LD, D_DU, D_LR, D_LU, D_RD); // weight with L<->D switch
w2 = wf5 (D_DU, D_LR, D_LU, D_RD, D_RU, D_LD); // weight with R<->D switch
if (w0 <= w1)
{
if (w0 <= w2) // w0 <= w1,w2
{
*weight = 0.0;
return (NONE);
}
else // w2 < w0 <= w1
{
*weight = w2 - w0;
if (verbose > 2 && !isBoostrap)
{
Debug ( (char*)"Possible swap across '%s'. Weight dropping by %f.", e->label, w0 - w2);
Debug ( (char*)"New tree length should be %f.", T->weight + w2 - w0);
}
return (RIGHT);
}
}
else if (w2 <= w1) // w2 <= w1 < w0
{
*weight = w2 - w0;
if (verbose > 2 && !isBoostrap)
{
Debug ( (char*)"Possible swap across '%s'. Weight dropping by %f.", e->label, w0 - w2);
Debug ( (char*)"New tree length should be %f.", T->weight + w2 - w0);
}
return(RIGHT);
}
else // w1 < w2, w0
{
*weight = w1 - w0;
if (verbose > 2 && !isBoostrap)
{
Debug ( (char*)"Possible swap across '%s'. Weight dropping by %f.", e->label, w0 - w1);
Debug ( (char*)"New tree length should be %f.", T->weight + w1 - w0);
}
return(LEFT);
}
}
void updateSubTreeAfterNNI (double **A, node *v, edge *rootEdge,
node *closer, node *further, double dcoeff, int direction)
{
edge *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;
}
return;
}