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"); }