void NormalizingReader::Clear()
{
writtenBlocks.clear();
blockMapper.clear();
for (VecBlockPtr::iterator it = blocksToDelete.begin(); it != blocksToDelete.end(); ++it)
delete *it;
}
void NxsReader::BlockReadHook(const NxsString &currBlockName, NxsBlock *currentBlock, NxsToken * token)
{
VecBlockPtr implied = currentBlock->GetImpliedBlocks();
for (VecBlockPtr::iterator impIt = implied.begin(); impIt != implied.end(); ++impIt)
{
NxsBlock * nb = *impIt;
NCL_ASSERT(nb);
NxsString impID = nb->GetID();
bool storeBlock = true;
if (destroyRepeatedTaxaBlocks && impID.EqualsCaseInsensitive("TAXA"))
{
NxsTaxaBlockAPI * oldTB = this->GetOriginalTaxaBlock((NxsTaxaBlockAPI *) nb);
if (oldTB)
{
storeBlock = ! currentBlock->SwapEquivalentTaxaBlock(oldTB);
const std::string altTitle = nb->GetTitle();
this->RegisterAltTitle(oldTB, altTitle);
if (!storeBlock)
{
delete nb;
}
}
}
if (storeBlock)
{
std::cerr << "storing implied block: " << impID << std::endl;
this->AddBlockToUsedBlockList(impID, nb, token);
}
}
std::cerr << "storing read block: " << currentBlock->GetID() << std::endl;
this->AddBlockToUsedBlockList(currBlockName, currentBlock, token);
}
void NormalizingReader::PostBlockReadingHook(NxsBlock & block)
{
//cerr << "PostBlockReadingHook for " << GetBlockIDTitleString(block) << endl;
NxsBlock * toStore;
if (this->storingBlocks)
{
try {
toStore = block.CloneBlock(blockMapper);
}
catch (...)
{
cerr << "CloneBlock of " << GetBlockIDTitleString(block) << " failed with an exception. Only Clonable blocks can be normalized." << endl;
throw;
}
blocksToDelete.push_back(toStore);
blockMapper[block.GetInstanceIdentifier()] = toStore;
}
else
toStore = █
VecBlockPtr impliedBlocks = toStore->GetImpliedBlocks();
for (VecBlockPtr::const_iterator ibIt = impliedBlocks.begin(); ibIt != impliedBlocks.end(); ++ibIt)
{
const BlockUniqueID currBlockID = (*ibIt)->GetInstanceIdentifier();
if ((!this->supportingSharedImpliedBlocks) || writtenBlocks.find(currBlockID) == writtenBlocks.end())
{
if (this->storingBlocks)
blocksToDelete.push_back(*ibIt);
try {
if (outf != 0L)
(*ibIt)->WriteAsNexus(*outf);
}
catch (...)
{
cerr << block.GetInstanceName() << "raised an exception when writing as NEXUS." << endl;
throw;
}
if (this->supportingSharedImpliedBlocks)
writtenBlocks.insert(currBlockID);
}
}
const BlockUniqueID toStoreBlockID = toStore->GetInstanceIdentifier();
try {
if (outf != 0L)
toStore->WriteAsNexus(*outf);
}
catch (...)
{
cerr << GetBlockIDTitleString(block) << " raised an exception when writing as NEXUS." << endl;
throw;
}
writtenBlocks.insert(toStoreBlockID);
}