std::string StackTrace::ToString() const {
std::stringstream stream;
#if !defined(__UCLIBC__)
OutputToStream(&stream);
#endif
return stream.str();
}
void Word::OutputToStream(
const ManagerBase &mgr,
size_t targetPos,
const SCFG::Hypothesis &hypo,
std::ostream &out) const
{
const SCFG::TargetPhraseImpl &tp = hypo.GetTargetPhrase();
const SCFG::SymbolBind &symbolBind = hypo.GetSymbolBind();
bool outputWord = true;
if (mgr.system.options.input.placeholder_factor != NOT_FOUND) {
const AlignmentInfo &alignInfo = tp.GetAlignTerm();
std::set<size_t> sourceAligns = alignInfo.GetAlignmentsForTarget(targetPos);
if (sourceAligns.size() == 1) {
size_t sourcePos = *sourceAligns.begin();
/*
cerr << "sourcePos=" << sourcePos << endl;
cerr << "tp=" << tp.Debug(mgr.system) << endl;
cerr << "m_symbolBind=" << symbolBind.Debug(mgr.system) << endl;
*/
assert(sourcePos < symbolBind.GetSize());
const Range &inputRange = symbolBind.coll[sourcePos].GetRange();
assert(inputRange.GetNumWordsCovered() == 1);
const SCFG::Sentence &sentence = static_cast<const SCFG::Sentence &>(mgr.GetInput());
const SCFG::Word &sourceWord = sentence[inputRange.GetStartPos()];
const Factor *factor = sourceWord[mgr.system.options.input.placeholder_factor];
if (factor) {
out << factor->GetString();
outputWord = false;
}
}
}
if (outputWord) {
OutputToStream(mgr.system, out);
}
}
bool ChemDrawXMLFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
static const xmlChar C_MOLECULE[] = "fragment";
static const xmlChar C_CDXML[] = "CDXML";
static const xmlChar C_BONDLENGTH[] = "BondLength";
static const xmlChar C_PAGE[] = "page";
static const xmlChar C_ATOM[] = "n";
static const xmlChar C_BOND[] = "b";
static const xmlChar C_ID[] = "id";
static const xmlChar C_CHARGE[] = "Charge";
static const xmlChar C_COORDS[] = "p";
static const xmlChar C_ELEMENT[] = "Element";
static const xmlChar C_ORDER[] = "Order";
static const xmlChar C_BEGIN[] = "B";
static const xmlChar C_END[] = "E";
static const xmlChar C_DISPLAY[] = "Display";
_pxmlConv = XMLConversion::GetDerived(pConv,false);
if(!_pxmlConv)
return false;
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
OBMol &mol = *pmol;
OBBond *pbond;
vector<OBBond*>::iterator j;
if(_pxmlConv->GetOutputIndex() == 1)
{
xmlTextWriterStartDocument(writer(), NULL, NULL, NULL);
xmlTextWriterWriteDTD(writer(), BAD_CAST "CDXML", NULL, BAD_CAST "http://www.camsoft.com/xml/cdxml.dtd", NULL);
xmlTextWriterStartElement(writer(), C_CDXML);
xmlTextWriterWriteFormatAttribute(writer(), C_BONDLENGTH , "30");
xmlTextWriterStartElement(writer(), C_PAGE); // put everything on one page
// now guess the average bond size for the first molecule and scale to 30.
_scale = 0.;
if (mol.NumBonds())
{
for (pbond = mol.BeginBond(j); pbond; pbond = mol.NextBond(j))
_scale += pbond->GetLength();
_scale /= mol.NumBonds();
}
else
_scale = 1.; // FIXME: what happens if the molecule has no bond?
_scale = 30. / _scale;
_offset = 0;
}
xmlTextWriterStartElement(writer(), C_MOLECULE);
OBAtom *patom;
vector<OBAtom*>::iterator i;
int n;
for (patom = mol.BeginAtom(i); patom; patom = mol.NextAtom(i))
{
xmlTextWriterStartElement(writer(), C_ATOM);
xmlTextWriterWriteFormatAttribute(writer(), C_ID , "%d", patom->GetIdx() + _offset);
xmlTextWriterWriteFormatAttribute(writer(), C_COORDS , "%f %f", patom->GetX() * _scale, patom->GetY() * _scale);
n = patom->GetAtomicNum();
if (n != 6)
{
xmlTextWriterWriteFormatAttribute(writer(), C_ELEMENT , "%d", n);
}
n = patom->GetFormalCharge();
if (n != 0)
{
xmlTextWriterWriteFormatAttribute(writer(), C_CHARGE , "%d", n);
}
xmlTextWriterEndElement(writer());
}
for (pbond = mol.BeginBond(j); pbond; pbond = mol.NextBond(j))
{
xmlTextWriterStartElement(writer(), C_BOND);
patom = pbond->GetBeginAtom();
xmlTextWriterWriteFormatAttribute(writer(), C_BEGIN , "%d", patom->GetIdx() + _offset);
patom = pbond->GetEndAtom();
xmlTextWriterWriteFormatAttribute(writer(), C_END , "%d", patom->GetIdx() + _offset);
n = pbond->GetBO();
if (n != 1)
{
xmlTextWriterWriteFormatAttribute(writer(), C_ORDER , "%d", n);
}
if (pbond->IsHash())
xmlTextWriterWriteFormatAttribute(writer(), C_DISPLAY , "WedgeBegin");
else if (pbond->IsWedge())
xmlTextWriterWriteFormatAttribute(writer(), C_DISPLAY , "WedgedHashEnd");
xmlTextWriterEndElement(writer());
}
_offset += mol.NumAtoms ();
xmlTextWriterEndElement(writer());//molecule
//TODO: Writing property block
if(_pxmlConv->IsLast())
{
xmlTextWriterEndDocument(writer()); // page
xmlTextWriterEndDocument(writer()); //document
OutputToStream();
}
return true;
}
std::string StackTrace::ToString() const {
std::stringstream stream;
OutputToStream(&stream);
return stream.str();
}
void StackTrace::PrintBacktrace()
{
OutputToStream(&std::cerr);
}
