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); }