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());
}
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);
}
