void me_o(double *X, int *N, char **labels, char **treeStr, int *nni)
{
double **D, **A;
set *species, *slooper;
node *addNode;
tree *T;
char *str;
int n, nniCount;
n = *N;
T = NULL;
nniCount = 0;
species = (set *) malloc(sizeof(set));
species->firstNode = NULL;
species->secondNode = NULL;
str = (char *)R_alloc(MAX_INPUT_SIZE, sizeof(char));
/* added by EP */
if (strlen(str))
strncpy(str, "", strlen(str));
/* end */
D = loadMatrix (X, labels, n, species);
A = initDoubleMatrix(2 * n - 2);
for(slooper = species; NULL != slooper; slooper = slooper->secondNode)
{
addNode = copyNode(slooper->firstNode);
T = GMEaddSpecies(T,addNode,D,A);
}
makeOLSAveragesTable(T,D,A);
// Compute NNI
if (*nni == 1)
NNI(T,A,&nniCount,D,n);
assignOLSWeights(T,A);
NewickPrintTreeStr(T,str);
if (strlen (str) < MAX_INPUT_SIZE -1)
{
*treeStr = (char *)R_alloc(MAX_INPUT_SIZE, sizeof(char));
/* added by EP */
if (strlen(*treeStr))
strncpy(*treeStr, "", strlen(*treeStr));
/* end */
strncpy (*treeStr, str, strlen (str));
}
/* free (str); */
freeMatrix(D,n);
freeMatrix(A,2*n - 2);
freeSet(species);
freeTree(T);
T = NULL;
return;
}
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 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 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;
}
