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::writeSequences(const Genome* inParent,
const vector<const Genome*>& inChildren)
{
vector<const Genome*> inGenomes = inChildren;
inGenomes.push_back(inParent);
const Genome* outParent = _outAlignment->openGenome(inParent->getName());
(void)outParent;
assert(outParent != NULL && outParent->getNumBottomSegments() > 0);
string buffer;
for (hal_size_t i = 0; i < inGenomes.size(); ++i)
{
const Genome* inGenome = inGenomes[i];
Genome* outGenome = _outAlignment->openGenome(inGenome->getName());
if (inGenome == inParent || outGenome->getNumChildren() == 0)
{
SequenceIteratorConstPtr inSeqIt = inGenome->getSequenceIterator();
SequenceIteratorConstPtr end = inGenome->getSequenceEndIterator();
for (; inSeqIt != end; inSeqIt->toNext())
{
const Sequence* inSequence = inSeqIt->getSequence();
if (inSequence->getSequenceLength() > 0)
{
Sequence* outSequence = outGenome->getSequence(inSequence->getName());
assert(outSequence != NULL);
inSequence->getString(buffer);
outSequence->setString(buffer);
}
}
}
}
}
void SequenceRenameTest::createCallBack(Alignment *alignment) {
Genome *ancGenome = alignment->addRootGenome("AncGenome", 0);
vector<Sequence::Info> seqVec;
seqVec.push_back(Sequence::Info("seq1", 40, 20, 20));
seqVec.push_back(Sequence::Info("seq2", 50, 20, 20));
seqVec.push_back(Sequence::Info("anotherSeq", 60, 20, 20));
ancGenome->setDimensions(seqVec);
alignment->closeGenome(ancGenome);
ancGenome = alignment->openGenome("AncGenome");
ancGenome->getSequence("seq1")->setName("foobar");
ancGenome->getSequence("seq2")->setName("a_really_really_super_long_name");
ancGenome->getSequence("anotherSeq")->setName("short");
ancGenome->getSequence("short")->setName("again");
}
