void MappedSegmentMapDownTest::testBottomSegment(
AlignmentConstPtr alignment,
BottomSegmentIteratorConstPtr bottom,
hal_size_t childIndex)
{
const Genome* child = bottom->getGenome()->getChild(childIndex);
set<MappedSegmentConstPtr> results;
bottom->getMappedSegments(results, child, NULL, false);
CuAssertTrue(_testCase, results.size() == 1);
MappedSegmentConstPtr mseg = *results.begin();
CuAssertTrue(_testCase, mseg->getSource()->getGenome() ==
bottom->getGenome());
CuAssertTrue(_testCase, mseg->getSource()->getStartPosition() ==
bottom->getStartPosition());
CuAssertTrue(_testCase,
mseg->getSource()->getLength() == bottom->getLength());
CuAssertTrue(_testCase,
mseg->getSource()->getReversed() == bottom->getReversed());
TopSegmentIteratorConstPtr top = child->getTopSegmentIterator();
top->toChild(bottom, childIndex);
CuAssertTrue(_testCase, mseg->getGenome() == top->getGenome());
CuAssertTrue(_testCase,
mseg->getStartPosition() == top->getStartPosition());
CuAssertTrue(_testCase,
mseg->getLength() == top->getLength());
CuAssertTrue(_testCase,
mseg->getReversed() == top->getReversed());
}
void MappedSegmentMapUpTest::testTopSegment(AlignmentConstPtr alignment,
TopSegmentIteratorConstPtr top,
const string& ancName)
{
const Genome* parent = alignment->openGenome(ancName);
set<MappedSegmentConstPtr> results;
top->getMappedSegments(results, parent, NULL, false);
CuAssertTrue(_testCase, results.size() == 1);
MappedSegmentConstPtr mseg = *results.begin();
CuAssertTrue(_testCase, mseg->getSource()->getGenome() == top->getGenome());
CuAssertTrue(_testCase, mseg->getSource()->getStartPosition() ==
top->getStartPosition());
CuAssertTrue(_testCase,
mseg->getSource()->getLength() == top->getLength());
CuAssertTrue(_testCase,
mseg->getSource()->getReversed() == top->getReversed());
BottomSegmentIteratorConstPtr bottom = parent->getBottomSegmentIterator();
bottom->toParent(top);
// extra hop for when top is in grand child
if (bottom->getGenome() != parent)
{
TopSegmentIteratorConstPtr temp =
bottom->getGenome()->getTopSegmentIterator();
temp->toParseUp(bottom);
bottom->toParent(temp);
}
CuAssertTrue(_testCase, mseg->getGenome() == bottom->getGenome());
CuAssertTrue(_testCase,
mseg->getStartPosition() == bottom->getStartPosition());
CuAssertTrue(_testCase,
mseg->getLength() == bottom->getLength());
CuAssertTrue(_testCase,
mseg->getReversed() == bottom->getReversed());
}
