void MappedSegmentMapAcrossTest::testTopSegment(AlignmentConstPtr alignment,
TopSegmentIteratorConstPtr top)
{
const Genome* parent = top->getGenome()->getParent();
const Genome* other = top->getGenome()->getName() == "child1" ?
alignment->openGenome("child2") : alignment->openGenome("child1");
set<MappedSegmentConstPtr> results;
top->getMappedSegments(results, other, 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);
TopSegmentIteratorConstPtr sister = other->getTopSegmentIterator();
sister->toChildG(bottom, other);
CuAssertTrue(_testCase, mseg->getGenome() == sister->getGenome());
CuAssertTrue(_testCase,
mseg->getStartPosition() == sister->getStartPosition());
CuAssertTrue(_testCase,
mseg->getLength() == sister->getLength());
CuAssertTrue(_testCase,
mseg->getReversed() == sister->getReversed());
}
void MappedSegmentMapDupeTest::checkCallBack(AlignmentConstPtr alignment)
{
validateAlignment(alignment);
const Genome* parent = alignment->openGenome("parent");
const Genome* child1 = alignment->openGenome("child1");
const Genome* child2 = alignment->openGenome("child2");
TopSegmentIteratorConstPtr top = child1->getTopSegmentIterator();
set<MappedSegmentConstPtr> results;
top->getMappedSegments(results, child2, NULL, true);
// CuAssertTrue(_testCase, results.size() == 3);
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);
TopSegmentIteratorConstPtr sister = child2->getTopSegmentIterator();
sister->toChildG(bottom, child2);
CuAssertTrue(_testCase, mseg->getGenome() == sister->getGenome());
CuAssertTrue(_testCase,
mseg->getStartPosition() == sister->getStartPosition());
CuAssertTrue(_testCase,
mseg->getLength() == sister->getLength());
CuAssertTrue(_testCase,
mseg->getReversed() == sister->getReversed());
top = child2->getTopSegmentIterator();
results.clear();
sister = child1->getTopSegmentIterator();
top->getMappedSegments(results, child1, NULL, true);
CuAssertTrue(_testCase, results.size() == 3);
bool found[3] = {false};
set<MappedSegmentConstPtr>::iterator i = results.begin();
for (; i != results.end(); ++i)
{
MappedSegmentConstPtr mseg = *i;
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);
TopSegmentIteratorConstPtr sister = child2->getTopSegmentIterator();
sister->toChildG(bottom, child1);
CuAssertTrue(_testCase, mseg->getGenome() == sister->getGenome());
CuAssertTrue(_testCase,
mseg->getLength() == sister->getLength());
found[mseg->getArrayIndex()] = true;
}
CuAssertTrue(_testCase, found[0] == true);
CuAssertTrue(_testCase, found[1] == true);
CuAssertTrue(_testCase, found[2] == true);
}
