void TopSegmentSimpleIteratorTest::createCallBack(Alignment *alignment) {
Genome *ancGenome = alignment->addRootGenome("Anc0", 0);
size_t numChildren = 9;
for (size_t i = 0; i < numChildren; ++i) {
alignment->addLeafGenome("Leaf" + std::to_string(i), "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);
for (size_t i = 0; not tsIt->atEnd(); tsIt->toRight(), ++i) {
CuAssertTrue(_testCase, (size_t)tsIt->getTopSegment()->getArrayIndex() == i);
_topSegments[i].applyTo(tsIt);
}
}
void TopSegmentIsGapTest::createCallBack(Alignment *alignment) {
size_t numSequences = 3;
vector<Sequence::Info> seqVec(numSequences);
BottomSegmentIteratorPtr bi;
BottomSegmentStruct bs;
TopSegmentIteratorPtr ti;
TopSegmentStruct ts;
Genome *parent1 = alignment->addRootGenome("parent1");
Genome *child1 = alignment->addLeafGenome("child1", "parent1", 1);
// set up two genomes. each with three sequences. each sequence
// with 5 segments of length two. start with segment i in parent
// aligned with segment i in child.
for (size_t i = 0; i < numSequences; ++i) {
string name = "Sequence" + std::to_string(i);
seqVec[i] = Sequence::Info(name, 10, 5, 5);
}
parent1->setDimensions(seqVec);
child1->setDimensions(seqVec);
for (bi = parent1->getBottomSegmentIterator(); not bi->atEnd(); bi->toRight()) {
bs.set(bi->getBottomSegment()->getArrayIndex() * 2, 2);
bs._children.clear();
bs._children.push_back(pair<hal_size_t, bool>(bi->getBottomSegment()->getArrayIndex(), false));
bs.applyTo(bi);
}
for (ti = child1->getTopSegmentIterator(); not ti->atEnd(); ti->toRight()) {
ts.set(ti->getTopSegment()->getArrayIndex() * 2, 2, ti->getTopSegment()->getArrayIndex());
ts.applyTo(ti);
}
// insertion in middle (8th top segment)
bi = parent1->getBottomSegmentIterator(8);
ti = child1->getTopSegmentIterator(8);
assert(bi->getBottomSegment()->getChildIndex(0) == 8 && ti->getTopSegment()->getParentIndex() == 8);
bi->getBottomSegment()->setChildIndex(0, 9);
ti->getTopSegment()->setParentIndex(NULL_INDEX);
ti->toRight();
ti->getTopSegment()->setParentIndex(8);
// insertion at begining (10th top segment)
bi = parent1->getBottomSegmentIterator(10);
ti = child1->getTopSegmentIterator(10);
assert(bi->getBottomSegment()->getChildIndex(0) == 10 && ti->getTopSegment()->getParentIndex() == 10);
bi->getBottomSegment()->setChildIndex(0, 11);
ti->getTopSegment()->setParentIndex(NULL_INDEX);
ti->toRight();
ti->getTopSegment()->setParentIndex(10);
// just having a null parent is not enough for an insertion
bi = parent1->getBottomSegmentIterator(2);
ti = child1->getTopSegmentIterator(2);
assert(bi->getBottomSegment()->getChildIndex(0) == 2 && ti->getTopSegment()->getParentIndex() == 2);
ti->getTopSegment()->setParentIndex(NULL_INDEX);
}