void SPR(tree *T, double **D, double **A, int *count)
{
int i,j,k;
node *v;
/*FILE *treefile;*/
edge *e,*f;
/* char filename[MAX_LABEL_LENGTH];*/
double ***swapWeights;
double swapValue = 0.0;
swapWeights = (double ***)malloc(2*sizeof(double **));
makeBMEAveragesTable(T,D,A);
assignBMEWeights(T,A);
weighTree(T);
/*if (verbose)
printf("Before SPRs: tree length is %lf.\n",T->weight);*/
for(i=0;i<2;i++)
swapWeights[i] = initDoubleMatrix(T->size);
do
{
swapValue=0.0;
zero3DMatrix(swapWeights,2,T->size,T->size);
i = j = k = 0;
for(e=depthFirstTraverse(T,NULL);NULL!=e;e=depthFirstTraverse(T,e))
assignSPRWeights(e->head,A,swapWeights);
findTableMin(&i,&j,&k,T->size,swapWeights,&swapValue);
swapValue = swapWeights[i][j][k];
if (swapValue < -EPSILON)
{
// if (verbose)
// printf("New tree weight should be %lf.\n",T->weight + 0.25*swapValue);
v = indexedNode(T,j);
f = indexedEdge(T,k);
// if (verbose)
// printf("Swapping tree below %s to split edge %s with head %s and tail %s\n",
// v->parentEdge->label,f->label,f->head->label,f->tail->label);
SPRTopShift(T,v,f,2-i);
makeBMEAveragesTable(T,D,A);
assignBMEWeights(T,A);
weighTree(T);
(*count)++;
/*sprintf(filename,"tree%d.new",*count);*/
// if (verbose)
// printf("After %d SPRs, tree weight is %lf.\n\n",*count,T->weight);
/*treefile = fopen(filename,"w");
NewickPrintTree(T,treefile);
fclose(treefile);*/
}
} while (swapValue < -EPSILON);
for(i=0;i<2;i++)
freeMatrix(swapWeights[i],T->size);
free(swapWeights);
/*if (verbose)
readOffTree(T);*/
}
void SPR (tree *T, double **D, double **A, int *count, FILE *statfile)
{
int i, j, k;
node *v;
edge *e, *f;
double ***swapWeights;
double treeWeightBefore;
double swapValue = 0.0;
boolean firstSPR = TRUE;
swapWeights = (double ***) mCalloc (2, sizeof(double **));
makeBMEAveragesTable (T, D, A);
assignBMEWeights (T, A);
weighTree (T);
treeWeightBefore = T->weight;
for (i=0; i<2; i++)
swapWeights[i] = initDoubleMatrix (T->size);
do
{
swapValue = 0.0;
zero3DMatrix (swapWeights, 2, T->size, T->size);
i = j = k = 0;
for (e = depthFirstTraverse (T, NULL); NULL != e; e = depthFirstTraverse (T, e))
assignSPRWeights (e->head, A, swapWeights);
findTableMin (&i, &j, &k, T->size, swapWeights, &swapValue);
swapValue = swapWeights[i][j][k];
if (swapValue < -FLT_EPSILON)
{
if (firstSPR)
{
firstSPR = FALSE;
if (!isBoostrap)
{
if (verbose > 2)
Debug ( (char*)"Before SPR: tree length is %f.", treeWeightBefore);
else if (verbose > 1)
Message ( (char*)". Before SPR: tree length is %f.", treeWeightBefore);
}
}
if (verbose > 2 && !isBoostrap)
Debug ( (char*)"New tree length should be %f.", T->weight + 0.25 * swapValue);
v = indexedNode (T, j);
f = indexedEdge (T, k);
if (verbose > 2 && !isBoostrap)
{
if ((NULL == f->head->label) || (strlen (f->head->label) == 0))
{
if ((NULL == f->tail->label) || (strlen (f->tail->label) == 0))
Debug ( (char*)"Swapping tree below '%s' to split edge '%s' with internal head and tail.",
v->parentEdge->label, f->label);
else
Debug ( (char*)"Swapping tree below '%s' to split edge '%s' with internal head and tail '%s'.",
v->parentEdge->label, f->label, f->tail->label);
}
else
{
if ((NULL == f->tail->label) || (strlen (f->tail->label) == 0))
Debug ( (char*)"Swapping tree below '%s' to split edge '%s' with head '%s' and internal tail.",
v->parentEdge->label, f->label, f->head->label, f->tail->label);
else
Debug ( (char*)"Swapping tree below '%s' to split edge '%s' with head '%s' and tail '%s'.",
v->parentEdge->label, f->label, f->head->label, f->tail->label);
}
}
SPRTopShift (v, f, 2-i);
makeBMEAveragesTable (T, D, A);
assignBMEWeights (T, A);
weighTree (T);
(*count)++;
if (!isBoostrap)
{
if (verbose > 2)
Debug ( (char*)"SPR %5d: new tree length is %f.", *count, T->weight);
else if (verbose > 1)
Message ( (char*)". SPR %5d: new tree length is %f.", *count, T->weight);
}
}
} while (swapValue < -FLT_EPSILON);
for (i=0; i<2; i++)
freeMatrix (swapWeights[i], T->size);
free (swapWeights);
return;
}