void TopSegmentIteratorReverseTest::checkCallBack(AlignmentConstPtr alignment) { BottomSegmentIteratorConstPtr bi; TopSegmentIteratorConstPtr ti, ti2; const Genome* parent1 = alignment->openGenome("parent1"); const Genome* child1 = alignment->openGenome("child1"); ti = child1->getTopSegmentIterator(); bi = parent1->getBottomSegmentIterator(); ti2 = child1->getTopSegmentIterator(); ti2->toChild(bi, 0); CuAssertTrue(_testCase, ti->getStartPosition() == 0); CuAssertTrue(_testCase, ti->getLength() == 10); CuAssertTrue(_testCase, ti->getReversed() == false); CuAssertTrue(_testCase, ti2->getStartPosition() == 9); CuAssertTrue(_testCase, ti2->getLength() == 10); CuAssertTrue(_testCase, ti2->getReversed() == true); bi->slice(1, 3); ti2->toChild(bi, 0); CuAssertTrue(_testCase, bi->getStartPosition() == 1); CuAssertTrue(_testCase, bi->getLength() == 6); CuAssertTrue(_testCase, ti2->getStartPosition() == 8); CuAssertTrue(_testCase, ti2->getLength() == 6); string buffer; bi->getString(buffer); CuAssertTrue(_testCase, buffer == "CCTACG"); ti2->getString(buffer); CuAssertTrue(_testCase, buffer == "CACGTA"); bi = child1->getBottomSegmentIterator(); CuAssertTrue(_testCase, bi->getReversed() == false); ti->toParseUp(bi); CuAssertTrue(_testCase, ti->getStartPosition() == 0); CuAssertTrue(_testCase, ti->getLength() == 5); bi->toReverse(); ti->toParseUp(bi); CuAssertTrue(_testCase, ti->getStartPosition() == 4); CuAssertTrue(_testCase, ti->getLength() == 5); bi->toReverse(); CuAssertTrue(_testCase, bi->getReversed() == false); bi->toRight(); ti->toParseUp(bi); CuAssertTrue(_testCase, ti->getStartPosition() == 5); CuAssertTrue(_testCase, ti->getLength() == 5); bi->toReverse(); ti->toParseUp(bi); CuAssertTrue(_testCase, ti->getStartPosition() == 9); CuAssertTrue(_testCase, ti->getLength() == 5); }
void MappedSegmentMapDownTest::checkCallBack(AlignmentConstPtr alignment) { validateAlignment(alignment); const Genome* parent = alignment->openGenome("parent"); BottomSegmentIteratorConstPtr bottom = parent->getBottomSegmentIterator(); testBottomSegment(alignment, bottom, 0); testBottomSegment(alignment, bottom, 1); bottom->slice(1,2); testBottomSegment(alignment, bottom, 0); testBottomSegment(alignment, bottom, 1); bottom->toReverse(); testBottomSegment(alignment, bottom, 0); testBottomSegment(alignment, bottom, 1); }