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());
}
void TopSegmentIteratorParseTest::checkCallBack(AlignmentConstPtr alignment)
{
BottomSegmentIteratorConstPtr bi;
TopSegmentIteratorConstPtr ti;
// case 1
const Genome* case1 = alignment->openGenome("case1");
ti = case1->getTopSegmentIterator();
bi = case1->getBottomSegmentIterator();
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
CuAssertTrue(_testCase, bi->getLength() == ti->getLength());
bi->slice(3, 1);
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getLength() ==
bi->getBottomSegment()->getLength() - 4);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
CuAssertTrue(_testCase, bi->getLength() == ti->getLength());
// case 2
const Genome* case2 = alignment->openGenome("case2");
ti = case2->getTopSegmentIterator();
bi = case2->getBottomSegmentIterator(1);
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
bi->slice(1, 1);
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
// case 3
const Genome* case3 = alignment->openGenome("case3");
ti = case3->getTopSegmentIterator();
bi = case3->getBottomSegmentIterator();
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
bi->slice(2, 1);
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
// case 4
const Genome* case4 = alignment->openGenome("case4");
ti = case4->getTopSegmentIterator();
bi = case4->getBottomSegmentIterator(1);
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
bi->slice(2, 2);
ti->toParseUp(bi);
CuAssertTrue(_testCase, bi->getStartPosition() == ti->getStartPosition());
}
