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()); }