void GappedSegmentSimpleIteratorTest2::createCallBack(AlignmentPtr alignment) { addIdenticalParentChild(alignment, 2, 100, 5); Genome* parent = alignment->openGenome(alignment->getRootName()); Genome* child = parent->getChild(0); TopSegmentIteratorPtr ti = child->getTopSegmentIterator(); BottomSegmentIteratorPtr bi = parent->getBottomSegmentIterator(); hal_index_t i = 0; bool reversed = true; while (ti != child->getTopSegmentEndIterator()) { if (i % 5 == 0) { reversed = !reversed; if (reversed && i < (hal_index_t)(parent->getNumBottomSegments() - 1)) { makeInversion(ti, 5); } } ti->toRight(); bi->toRight(); ++i; } }
void GappedSegmentSimpleIteratorTest::createCallBack(AlignmentPtr alignment) { addIdenticalParentChild(alignment, 2, 100, 5); Genome* parent = alignment->openGenome(alignment->getRootName()); Genome* child = parent->getChild(0); TopSegmentIteratorPtr ti = child->getTopSegmentIterator(); BottomSegmentIteratorPtr bi = parent->getBottomSegmentIterator(); int i = 0; while (ti != child->getTopSegmentEndIterator()) { if (i++ % 2) { ti->getTopSegment()->setParentReversed(true); bi->getBottomSegment()->setChildReversed(0, true); } ti->toRight(); bi->toRight(); } }
void TopSegmentSimpleIteratorTest::createCallBack(AlignmentPtr alignment) { Genome* ancGenome = alignment->addRootGenome("Anc0", 0); size_t numChildren = 9; for (size_t i = 0; i < numChildren; ++i) { std::stringstream ss; ss << i; alignment->addLeafGenome(string("Leaf") + ss.str(), "Anc0", 0.1); } vector<Sequence::Info> seqVec(1); seqVec[0] = Sequence::Info("Sequence", 1000000, 5000, 10000); ancGenome->setDimensions(seqVec); CuAssertTrue(_testCase, ancGenome->getNumChildren() == numChildren); _topSegments.clear(); for (size_t i = 0; i < ancGenome->getNumTopSegments(); ++i) { TopSegmentStruct topSeg; topSeg.setRandom(); topSeg._length = ancGenome->getSequenceLength() / ancGenome->getNumTopSegments(); topSeg._startPosition = i * topSeg._length; _topSegments.push_back(topSeg); } TopSegmentIteratorPtr tsIt = ancGenome->getTopSegmentIterator(0); TopSegmentIteratorConstPtr tsEnd = ancGenome->getTopSegmentEndIterator(); for (size_t i = 0; tsIt != tsEnd; tsIt->toRight(), ++i) { CuAssertTrue(_testCase, (size_t)tsIt->getTopSegment()->getArrayIndex() == i); _topSegments[i].applyTo(tsIt); } }