void SequenceUpdateTest::createCallBack(Alignment *alignment) {
hal_size_t alignmentSize = alignment->getNumGenomes();
CuAssertTrue(_testCase, alignmentSize == 0);
Genome *ancGenome = alignment->addRootGenome("AncGenome", 0);
size_t numSequences = 1000;
vector<Sequence::Info> seqVec;
for (size_t i = 0; i < numSequences; ++i) {
hal_size_t len = 1 + i * 5 + i;
string name = "sequence" + std::to_string(i);
seqVec.push_back(Sequence::Info(name, len, i, i * 2));
}
ancGenome->setDimensions(seqVec);
alignment->closeGenome(ancGenome);
ancGenome = alignment->openGenome("AncGenome");
vector<Sequence::UpdateInfo> updateVec;
for (size_t i = 0; i < numSequences / 2; ++i) {
const Sequence *sequence = ancGenome->getSequence("sequence" + std::to_string(i));
updateVec.push_back(Sequence::UpdateInfo(sequence->getName(), i * 7));
}
ancGenome->updateTopDimensions(updateVec);
updateVec.clear();
for (size_t i = 0; i < numSequences / 3; ++i) {
const Sequence *sequence = ancGenome->getSequence("sequence" + std::to_string(i));
updateVec.push_back(Sequence::UpdateInfo(sequence->getName(), i * 5));
}
ancGenome->updateBottomDimensions(updateVec);
}
void LodExtract::writeDimensions(
const map<const Sequence*, hal_size_t>& segmentCounts,
const string& parentName,
const vector<string>& childNames)
{
// initialize a dimensions list for each (input) genome
map<const Genome*, vector<Sequence::Info> > dimMap;
map<const Genome*, vector<Sequence::Info> >::iterator dimMapIt;
vector<string> newGenomeNames = childNames;
newGenomeNames.push_back(parentName);
for (size_t i = 0; i < newGenomeNames.size(); ++i)
{
const Genome* inGenome = _inAlignment->openGenome(newGenomeNames[i]);
pair<const Genome*, vector<Sequence::Info> > newEntry;
newEntry.first = inGenome;
// it's important we keep the sequences in the output genome
// in the same order as the sequences in the input genome since
// we always use global coordinates!
SequenceIteratorConstPtr seqIt = inGenome->getSequenceIterator();
SequenceIteratorConstPtr seqEnd = inGenome->getSequenceEndIterator();
for (; seqIt != seqEnd; seqIt->toNext())
{
const Sequence* inSequence = seqIt->getSequence();
map<const Sequence*, hal_size_t>::const_iterator segMapIt;
segMapIt = segmentCounts.find(inSequence);
// we skip empty sequences for now with below check
if (segMapIt != segmentCounts.end())
{
vector<Sequence::Info>& segDims = newEntry.second;
hal_size_t nTop =
inGenome->getName() == parentName ? 0 : segMapIt->second;
hal_size_t nBot =
inGenome->getName() != parentName ? 0 : segMapIt->second;
segDims.push_back(Sequence::Info(inSequence->getName(),
inSequence->getSequenceLength(),
nTop,
nBot));
}
}
// note potential bug here for genome with no data
dimMap.insert(newEntry);
}
// now that we have the dimensions for each genome, update them in
// the output alignment
for (dimMapIt = dimMap.begin(); dimMapIt != dimMap.end(); ++dimMapIt)
{
Genome* newGenome = _outAlignment->openGenome(dimMapIt->first->getName());
assert(newGenome != NULL);
vector<Sequence::Info>& segDims = dimMapIt->second;
// ROOT
if (newGenome->getName() == _outAlignment->getRootName())
{
assert(newGenome->getName() == parentName);
newGenome->setDimensions(segDims, _keepSequences);
}
// LEAF
else if (newGenome->getName() != parentName)
{
newGenome->setDimensions(segDims, _keepSequences);
}
// INTERNAL NODE
else
{
vector<Sequence::UpdateInfo> updateInfo;
for (size_t i = 0; i < segDims.size(); ++i)
{
updateInfo.push_back(
Sequence::UpdateInfo(segDims[i]._name,
segDims[i]._numBottomSegments));
}
newGenome->updateBottomDimensions(updateInfo);
}
}
}
