vguard<vguard<LogProb> > SumProduct::logNodeExcludedPostProb (TreeNodeIndex node, TreeNodeIndex exclude, bool normalize) const {
Require (!isGap(node), "Attempt to find posterior probability of sequence at gapped position");
const UnvalidatedAlphTok tok = isWild(node) ? -1 : model.tokenize(gappedCol[node]);
vguard<LogProb> lppInit (model.alphabetSize(), isWild(node) ? 0 : -numeric_limits<double>::infinity());
if (!isWild(node))
lppInit[tok] = 0;
vguard<vguard<LogProb> > v (model.components(), lppInit);
LogProb norm = -numeric_limits<double>::infinity();
for (int cpt = 0; cpt < components(); ++cpt) {
vguard<LogProb>& lpp = v[cpt];
for (auto& lp: lpp)
lp += logCptWeight[cpt];
for (size_t nc = 0; nc < tree.nChildren(node); ++nc) {
const TreeNodeIndex child = tree.getChild(node,nc);
if (child != exclude)
for (AlphTok i = 0; i < model.alphabetSize(); ++i)
lpp[i] += log (E[cpt][child][i]) + logE[cpt][child];
}
const TreeNodeIndex parent = tree.parentNode (node);
for (AlphTok i = 0; i < model.alphabetSize(); ++i) {
lpp[i] += parent == exclude
? 0 // to add a prior for orphaned nodes, this should be log(insProb[i]), but that complicates MCMC etc
: (log(G[cpt][node][i]) + logG[cpt][node]);
log_accum_exp (norm, lpp[i]);
}
}
if (normalize)
for (auto& lpp: v)
for (auto& lp: lpp)
lp -= norm;
return v;
}
NxI32 deleteFiles(const String &str)
{
WildCard *wild = createWildCard(str.c_str());
StringVector list;
if ( isWild(wild) )
{
FileFind ffind(wild);
ffind.GetFiles(list);
}
else
{
list.push_back(str);
}
StringVector::iterator i;
for (i=list.begin(); i!=list.end(); ++i)
{
#ifdef WIN32
DeleteFileA( (*i).c_str() );
#endif
#ifdef LINUX_GENERIC
assert(0); // not implemented on unix yet, not needed though.
#endif
}
releaseWildCard(wild);
NxI32 ret = list.size();
return ret;
}
bool addFilename(StringAttrArray &names,const char *name,bool sub)
{
if (isWild(name)) {
StringBuffer dir;
const char *tail = splitDirTail(name,dir);
if (isWild(dir.str())) {
printf("Directory %s - cannot be wild!\n",dir.str());
return false;
}
Owned<IFile> dirf = createIFile(dir.str());
Owned<IDirectoryIterator> iter = dirf->directoryFiles(tail,sub,false);
StringBuffer subname;
ForEach(*iter) {
subname.clear().append(iter->query().queryFilename());
names.append(*new StringAttrItem(subname.str()));
}
}
else
