void getStartingTree(tree *tr, analdef *adef)
{
tr->likelihood = unlikely;
if(adef->restart)
{
INFILE = myfopen(tree_file, "rb");
if(!adef->grouping)
{
switch(adef->mode)
{
case ANCESTRAL_STATES:
assert(!tr->saveMemory);
tr->leftRootNode = (nodeptr)NULL;
tr->rightRootNode = (nodeptr)NULL;
treeReadLen(INFILE, tr, FALSE, FALSE, FALSE, adef, TRUE, FALSE);
assert(tr->leftRootNode && tr->rightRootNode);
break;
case CLASSIFY_MP:
treeReadLen(INFILE, tr, TRUE, FALSE, TRUE, adef, FALSE, FALSE);
break;
case OPTIMIZE_BR_LEN_SCALER:
treeReadLen(INFILE, tr, TRUE, FALSE, FALSE, adef, TRUE, FALSE);
break;
case CLASSIFY_ML:
if(adef->useBinaryModelFile)
{
if(tr->saveMemory)
treeReadLen(INFILE, tr, TRUE, FALSE, TRUE, adef, FALSE, FALSE);
else
treeReadLen(INFILE, tr, TRUE, FALSE, FALSE, adef, FALSE, FALSE);
}
else
{
if(tr->saveMemory)
treeReadLen(INFILE, tr, FALSE, FALSE, TRUE, adef, FALSE, FALSE);
else
treeReadLen(INFILE, tr, FALSE, FALSE, FALSE, adef, FALSE, FALSE);
}
break;
default:
if(tr->saveMemory)
treeReadLen(INFILE, tr, FALSE, FALSE, TRUE, adef, FALSE, FALSE);
else
treeReadLen(INFILE, tr, FALSE, FALSE, FALSE, adef, FALSE, FALSE);
break;
}
}
else
{
assert(adef->mode != ANCESTRAL_STATES);
partCount = 0;
if (! treeReadLenMULT(INFILE, tr, adef))
exit(-1);
}
if(adef->mode == PARSIMONY_ADDITION)
return;
if(adef->mode != CLASSIFY_MP)
{
if(adef->mode == OPTIMIZE_BR_LEN_SCALER)
{
assert(tr->numBranches == tr->NumberOfModels);
scaleBranches(tr, TRUE);
evaluateGenericInitrav(tr, tr->start);
}
else
{
evaluateGenericInitrav(tr, tr->start);
treeEvaluate(tr, 1);
}
}
fclose(INFILE);
}
else
{
assert(adef->mode != PARSIMONY_ADDITION &&
adef->mode != MORPH_CALIBRATOR &&
adef->mode != ANCESTRAL_STATES &&
adef->mode != OPTIMIZE_BR_LEN_SCALER);
if(adef->randomStartingTree)
makeRandomTree(tr, adef);
else
makeParsimonyTree(tr, adef);
if(adef->startingTreeOnly)
{
printStartingTree(tr, adef, TRUE);
exit(0);
}
else
printStartingTree(tr, adef, FALSE);
evaluateGenericInitrav(tr, tr->start);
treeEvaluate(tr, 1);
}
tr->start = tr->nodep[1];
}
void getStartingTree(tree *tr, analdef *adef)
{
tr->likelihood = unlikely;
if(adef->restart)
{
INFILE = myfopen(tree_file, "rb");
if(!adef->grouping)
{
if(tr->saveMemory)
treeReadLen(INFILE, tr, FALSE, FALSE, TRUE, adef, FALSE);
else
treeReadLen(INFILE, tr, FALSE, FALSE, FALSE, adef, FALSE);
}
else
{
partCount = 0;
if (! treeReadLenMULT(INFILE, tr, adef))
exit(-1);
}
if(adef->mode == PARSIMONY_ADDITION)
return;
{
/*
double t = gettime();
int i;
for(i = 0; i < 50; i++)
*/
evaluateGenericInitrav(tr, tr->start);
/*
printf("%1.40f \n", tr->likelihood);
printf("%f\n", gettime() - t);
*/
treeEvaluate(tr, 1);
/*
printf("%1.40f \n", tr->likelihood);
printf("%f\n", gettime() - t);
exit(1);
*/
}
fclose(INFILE);
}
else
{
assert(adef->mode != PARSIMONY_ADDITION &&
adef->mode != MORPH_CALIBRATOR &&
adef->mode != MORPH_CALIBRATOR_PARSIMONY);
if(adef->randomStartingTree)
makeRandomTree(tr, adef);
else
makeParsimonyTree(tr, adef);
if(adef->startingTreeOnly)
{
printStartingTree(tr, adef, TRUE);
exit(0);
}
else
printStartingTree(tr, adef, FALSE);
setupPointerMesh(tr);
evaluateGenericInitrav(tr, tr->start);
treeEvaluate(tr, 1);
}
tr->start = tr->nodep[1];
}
