void GappedBottomSegmentIterator::toRightNextUngapped(TopSegmentIteratorPtr topSeqIt) const {
while (topSeqIt->tseg()->hasParent() == false && topSeqIt->getLength() <= _gapThreshold) {
if ((!topSeqIt->getReversed() && topSeqIt->getTopSegment()->isLast()) ||
(topSeqIt->getReversed() && topSeqIt->getTopSegment()->isFirst())) {
break;
}
topSeqIt->toRight();
}
}
void TopSegmentSimpleIteratorTest::checkCallBack(const Alignment *alignment) {
const Genome *ancGenome = alignment->openGenome("Anc0");
CuAssertTrue(_testCase, ancGenome->getNumTopSegments() == _topSegments.size());
TopSegmentIteratorPtr tsIt = ancGenome->getTopSegmentIterator(0);
for (size_t i = 0; i < ancGenome->getNumTopSegments(); ++i) {
CuAssertTrue(_testCase, (size_t)tsIt->getTopSegment()->getArrayIndex() == i);
_topSegments[i].compareTo(tsIt, _testCase);
tsIt->toRight();
}
tsIt = ancGenome->getTopSegmentIterator(ancGenome->getNumTopSegments() - 1);
for (hal_index_t i = ancGenome->getNumTopSegments() - 1; i >= 0; --i) {
CuAssertTrue(_testCase, tsIt->getTopSegment()->getArrayIndex() == i);
_topSegments[i].compareTo(tsIt, _testCase);
tsIt->toLeft();
}
tsIt = ancGenome->getTopSegmentIterator(0);
tsIt->slice(0, tsIt->getLength() - 1);
for (hal_index_t i = 0; i < (hal_index_t)ancGenome->getSequenceLength(); ++i) {
CuAssertTrue(_testCase, tsIt->getLength() == 1);
CuAssertTrue(_testCase, tsIt->getStartPosition() == i);
tsIt->toRight(tsIt->getStartPosition() + 1);
}
tsIt = ancGenome->getTopSegmentIterator(ancGenome->getNumTopSegments() - 1);
tsIt->slice(tsIt->getLength() - 1, 0);
for (hal_index_t i = ancGenome->getSequenceLength() - 1; i >= 0; --i) {
CuAssertTrue(_testCase, tsIt->getLength() == 1);
CuAssertTrue(_testCase, tsIt->getStartPosition() == i);
tsIt->toLeft(tsIt->getStartPosition() - 1);
}
tsIt = ancGenome->getTopSegmentIterator(0);
tsIt->toReverse();
CuAssertTrue(_testCase, tsIt->getReversed() == true);
tsIt->slice(tsIt->getLength() - 1, 0);
for (hal_index_t i = 0; i < (hal_index_t)ancGenome->getSequenceLength(); ++i) {
CuAssertTrue(_testCase, tsIt->getLength() == 1);
CuAssertTrue(_testCase, tsIt->getStartPosition() == i);
tsIt->toLeft(tsIt->getStartPosition() + 1);
}
tsIt = ancGenome->getTopSegmentIterator(ancGenome->getNumTopSegments() - 1);
tsIt->toReverse();
tsIt->slice(0, tsIt->getLength() - 1);
for (hal_index_t i = ancGenome->getSequenceLength() - 1; i >= 0; --i) {
CuAssertTrue(_testCase, tsIt->getLength() == 1);
CuAssertTrue(_testCase, tsIt->getStartPosition() == i);
tsIt->toRight(tsIt->getStartPosition() - 1);
}
}